WO2015013191A1 - Methods, systems, apparatus and their optimization for effective clinical analysis and conveying results thereof - Google Patents

Abstract

Disclosed are methods, systems, apparatus, e.g. computational and technological methods, systems, apparatus and components thereof and their optimization to arrive at effective clinical analysis of diseases or ailments, e.g. cancer, so that a subject suffering from the disease or ailment and in need of therapeutic intervention for that disease or ailment may be provided with personalized treatment options or considerations.

Description

METHODS, SYSTEMS, APPARATUS AND THEIR OPTIMIZATION FOR EFFECTIVE CLINICAL ANALYSIS AND CONVEYING RESULTS THEREOF

RELATED APPLICATIONS AND INCORPORATION BY REFERENCE

[0Θ01] This application claims priority to and benefit of US provisional patent application Serial No. 61/856,738 filed July 21, 2013 and US provisional patent application Serial No. 61/996,874 filed May 16, 2014.

[0002] The foregoing application, and all documents cited therein or during their prosecution ("appin cited documents") and all documents cited or referenced in the appin cited documents, and all documents cited or referenced herein ("herein cited documents"), and all documents cited or referenced in herein cited documents, together with any manufacturer's instructions, descriptions, product specifications, and product sheets for any products mentioned herein or in any document incorporated by reference herein, are hereby incorporated herein by reference, and may be employed in the practice of the invention. More specifically, all referenced documents are incorporated by reference to the same extent as if each individual document was specifically and individually indicated to be incorporated by reference.

FIELD OF THE INVENTION

[0003] The present invention generally relates to methods, systems, apparatus, e.g., computational and technological methods, systems, apparatus and components thereof and their optimization to arrive at effective clinical analysis of diseases or ailments, e.g., cancer, so that a subject suffering from the disease or ailment and in need of therapeutic intervention for that disease or ailment may be provided with personalized treatment options or considerations.

STATEMENT AS TO FEDERALLY SPONSORED RESEARCH

[0004J This invention was made with government support, provided by the Starr Cancer Foundation, the Prostate Cancer Foundation, US National institutes of Health (NIH) NHGRI Clinical Sequencing Exploratory Research grant 1U01HG006492, the NIH National Cancer Institute and NHGRI grant 1 U24CA 126546, the US Department of Defense, NIH U24CA143845 grant and the Dana-Farber Leadership Council). The government has certain rights in the invention. BACKGROUND OF THE INVENTION

[0005] Cancer or the synonymous term malignant neoplasm refers to a broad group of diseases that relate to unregulated cell growth. In cancer, abnormal cells divide without control to form malignant tumors, and may invade nearby parts of the body. Cancer cells may also spread to more distant parts of the body through the lymphatic system or bloodstream. There are over 200 different known cancers that afflict humans.

[0006] Cancers may be divided into multiple categories, the main types being Carcinomas, Sarcomas, Leukemias, Lymphomas and myelomas and Central nervous system cancers, e.g., gliomas. Carcinoma is a type of cancer that begins in the skin or in tissues that line or cover internal organs. Subtypes of carcinoma, include but are not limited to adenocarcinoma, basal cell carcinoma, squamous cell carcinoma, and transitional cell carcinoma. Sarcoma is a type of cancer that begins in bone, cartilage, fat, muscle, blood vessels, or other connective or supportive tissue. Leukemia is a type of cancer that starts in blood-forming tissue such as the bone marrow and causes large numbers of abnormal blood cells to be produced and enter the blood. Lymphoma and myeloma are types of cancers that begin in the cells of the immune system and Central nervous system cancers are cancers that begin in the tissues of the brain and spinal cord. Not all tumors are cancerous as benign tumors are not known to grow uncontrollably, invade neighboring tissues or spread throughout the body. Also not all. cancers form tumors, e.g., Leukemia.

[0007] Since cancer is fundamentally a disease of failure of regulation of tissue growth, for a normal cell to transform into a cancer ceil, the genes which regulate cell growth and differentiation must be altered. The affected genes may be divided into two broad categories. Oncogenes are genes which promote cell growth and reproduction. Tumor suppressor genes are genes which inhibit cell division and survival. Malignant transformation can occur through the formation of novel oncogenes, the inappropriate over-expression of normal oncogenes, or by the under-expression or disabling of tumor suppressor genes. Typically, changes in many genes are required to transform a normal cell into a cancer cell, and these genetic changes can occur at different levels and by different mechanisms. The gain or loss of an entire chromosome can occur through errors in mitosis. More common are mutations, which are changes in the nucleotide sequence of genomic DNA. [0008] Large-scale mutations involve the deletion or gain of a portion of a chromosome. Genomic amplification occurs when a cell gains many copies (often 20 or more) of a small chromosomal locus, usually containing one or more oncogenes and adjacent genetic material. Translocation occurs when two separate chromosomal regions become abnormally fused, often at a characteristic location. Small-scale mutations include point mutations, deletions, and insertions, which may occur in the promoter region of a gene and affect its expression, or may occur in the gene's coding sequence and alter the function or stability of its protein product. Disruption of a single gene may also result from integration of genomic material from a DNA virus or retrovims, and resulting in the expression of viral oncogenes in the affected cell and its descendants.

[0009] Replication of the enormous amount of data contained within the DNA of living cells may result in some mutations as well. Complex error correction and prevention is built into the process, and safeguards the cell against cancer. If significant error occurs, the damaged cell can "self-destruct" through programmed cell death or apoptosis. If the error control processes fail, then the mutations will survive and be passed along to daughter cells. Some environments make errors more likely to arise and propagate. Such environments can include the presence of disruptive substances called carcinogens, repeated physical injury, heat, ionizing radiation, or hypoxia. Cancer may also be driven by epigenetic alterations which refer to functionally relevant modifications to the genome that do not involve a change in the nucleotide sequence. Examples of such modifications are changes in DNA methylation (hypermethylation and hypomethylation) and histoiie modification and changes in chromosomal architecture. Each of these epigenetic alterations serves to regulate gene expression without altering the underlying DNA sequence. These changes may remain through cell divisions, last for multiple generations, and can be considered to be epimutations. Cancers usually arise from an assemblage of mutations and epimutations leading to clonal expansion whereby cancer cells are conferred a selective competitive reproductive or survival advantage over other cells in the tissue. Though there is no single cure for cancer, cancer management including but not limited to surgery, chemotherapy, radiation therapy, and palliative care play important roles in keeping disease progression in check.

[0010] In the year 2013, the National Cancer Institute at the National Institutes of Health reported that there were an estimated 1,660,290 new cases of cancer (not including nonmelanoma skin cancers) in the United States and 580,350 new deaths associated with cancer. On a global scale, in 2008 approximately 12.7 million cancers were diagnosed (not including non-melanoma skin cancers and other non-invasive cancers) and in 2010 nearly 7.98 million people died.

[0Θ11] Due to enormous efforts in genomics, bioinformatics and development of next generation sequencing technologies, the past several years have seen numerous computational and technological advances in the characterization of mutations, e.g., point mutations and structural alterations associated with a number of cancers, providing researchers with a more comprehensive view of cancer development. Most prospective clinical genotyping efforts have utilized on "hotspot" genotyping or targeted sequencing panels of clinically relevant genes using either fresh frozen or formalin-fixed, paraffin-embedded (FFPE) tissue. Pilot studies that apply research-grade massively parallel sequencing technology in focused clinical settings have also been reported. However, multiple challenges to widespread clinical implementation of Whole- exome sequencing (WES) remain unaddressed. One challenge involves generating high-quality WES data from archival FFPE tumor material in a clinically relevant time frame. Another involves clinically interpreting exome-scale genomic data for prospective clinical use that maximizes its clinical and biological exploration. A third involves developing a system to interrogate plausibly actionable variants of uncertain significance. Overcoming these challenges may allow rigorous assessment of the value of large-scale tumor genomic information to guide clinical decision-making and inform selected experimental follow-up.

[0012] Citation or identification of any document in this application is not an admission that such document is avai lable as prior art to the present invention.

SUMMARY OF THE INVENTION

[0013] There is a need to develop approaches that generate high-quality WES data from archival tumor material and validate FFPE WES sequencing data with corresponding frozen WES. There is a further need to develop computational methods, e.g., heuristic algorithms that interpret the resulting data for clinical oncologists, and establish the clinical applicability of this interpretation algorithm. Applicants have shown that prospective application of their novel platform to a series of patients representing a range of tumor types indicates that this approach enables both biological discovery and clinical trial enrollment and may therefore facilitate widespread application of WES for precision cancer medicine studies. It is critical to develop and optimize computational methods, systems and apparatus that can arrive at an effective clinical analysis of an individual patient's cancer that has a higher chance of providing personalized treatment to said cancer patient to improve disease prognosis.

[0Θ14] WES has been applied widely to advance cancer genomics and therapeutic development. Translating WES for prospective clinical use may impact the care of cancer patients; however, multiple scientific and technical innovations are necessary for its successful clinical implementation. These include: (1) rapid and robust WES from small amounts of formalin-fixed paraffin embedded (FFPE) tumor tissue, (2) analytical output that is equivalent to data from frozen samples, and (3) clinical interpretation of WES d ata for prospective use.

[0015] Aspects of the invention comprehend a prospective clinical WES platform that detects genomic alterations in archival FFPE tumor samples in a clinically appropriate time frame. The platform employs computational methods optimized for effective clinical analysis and interpretation of WES data. When applied to a retrospective cohort of 511 exomes, this interpretative framework revealed a "long tail" of somatic alterations in clinically important genes. Prospective application of this approach identified clinically relevant alterations in 15/16 patients. Previously undetected findings guided clinical trial enrollment that led to an objective clinical response. Applicants also demonstrate and apply an approach for experimental validation of novel alterations to expand the spectrum of clinically relevant somatic alterations. Overall, Applicants' novel methodology may inform the widespread implementation of precision cancer medicine.

[0016] An aspect of the invention comprehends methods of evaluating and ranking genomic alterations in tumor tissue comprising identifying somatic gene variants having clinical or biological relevance for personalized patient tumor treatment options for treating a patient in need of tumor treatment, comprising the steps of: (a) as to tumor tissue of the patient ("patient tumor tissue") that has been subjected to whole exome-sequencing and archival tumor tissue samples that have been subjected to whole-exome sequencing (i) determining concordance of mutations observed in patient tumor tissue that are observed in archival tumor samples and (ii) determining concordance of mutations observed in archival tumor samples that are observed in patient tumor tissue, whereby somatic variants are obtained; (b) generating or accessing a database of genes having therapeutic, prognostic or diagnostic implications for cancer patients or patients having tumors; (c) sorting each somatic variant obtained in step (a) by clinical and biological relevance; (d) linking genes from the database generated or accessed in step (b) with additional biological significant gene data; and (e) demoting variants of uncertain significance, or promoting certain variants of significance; whereby variants of significance are identified and somatic gene alterations having clinical or biological relevance are identified for personalized patient treatment options.

[0017] In an embodiment of the invention, the whole-exome sequencing comprises whole- exome sequencing on formalin- fixed paraffin embedded (FFPE) patient tumor tissue. In one aspect, the tumor is a solid tumor. In one aspect, the tumor is a liquid tumor. In one aspect, the tumor is a cancer of one or more tissues selected from, but not limited to, skin, brain, spinal and other nervous tissue, skeleton, heart, thyroid, lung, liver, spleen, pancreas, kidney, adrenal glands, liver, bladder, gall bladder, breast, muscle, gastrointestinal tract (including without limitation oral cavity, tongue, esophagus, stomach, gut, intestine, colon, rectum), reproductive tract (including without limitation ovary, fallopian tube, uterus, cervix, prostate, penis) and blood cancers including without limitation leukemia, myelomas and lymphoma. In one aspect, the tumor is benign. In one aspect, the tumor is pre-metastatic. In one aspect, the tumor is metastatic.

[0018] In a further embodiment of the invention the tumor comprises gastrointestinal stromal tumors, or skin, for example squamous cell carcinoma; a hematopoieitic tumor of lymphoid lineage, for example leukemia, acute lymphocytic leukemia, chronic lymphocytic leukemia, B- cell lymphoma (such as diffuse large B cell lymphoma), T-cell lymphoma, Hodgkin's lymphoma, non-Hodgkin's lymphoma, hairy cell lymphoma, or Burkitt's lymphoma; a hematopoieitic tumor of myeloid lineage, including, but not limited to acute myeloid leukemia, chronic myeloid leukemias, myelogenous leukemias, and Imatinib sensitive and refractory chronic myelogenous leukemias, myelodysplastic syndrome, Bortezomib sensitive and refractory multiple myeloma, myeloproliferative disease or promyelocytic leukaemia; thyroid follicular cancer; a tu or of mesenchymal origin, for exampl e fibrosarcoma or rhabdomyosarcoma; a tumour of the central or peripheral nervous system, for example astrocytoma, neuroblastoma, glioma (a High grade glioma) or schwannoma; melanoma (e.g., malignant or metastatic melanoma); seminoma; teratocarcinoma; osteosarcoma; kerato acanthoma; thyroid follicular cancer; Kaposi's sarcoma or Ewing's sarcoma. [0019] In a still further embodiment of the invention the demoting and promoting of somatic variants is based on scoring modifications for known mutations, missense mutations in protein kinase regions, copy number alterations with directionality known to have clinical impact, presence of recurrent alterations in a known database, presence in the pathway of concurrently altered actionable genes in the same sample using curated cancer pathways from a known database, or presence in known cancer pathways, gene sets, or modules identified in a known database.

[0020] A further aspect of the invention comprehends methods of evaluating and ranking genomic alterations in tumor tissue comprising identifying somatic gene variants having clinical or biological relevance for personalized patient tumor treatment options for treating a patient in need of tumor treatment, comprising the steps of: (a) performing whole-exome sequencing on tumor tissue of the patient ("patient tumor tissue"); (b) performing whole-exome sequencing on archival tumor tissue samples; (c) (i) determining concordance of mutations observed in patient tumor tissue that are observed in archival tumor samples and (ii) determining concordance of mutations observed in archival tumor samples that are observed in patient tumor tissue, whereby somatic variants are obtained; (d) generating or accessing a database of genes having therapeutic, prognostic or diagnostic implications for cancer patients; (e) sorting each somatic variant obtained in step (c) by clinical and biological relevance; (f) linking genes from the database generated or accessed in step (d) with additional biological significant gene data; and (g) demoting variants of uncertain significance, or promoting certain variants of significance; whereby variants of significance are identified and somatic gene alterations having clinical or biological relevance are identified for personalized patient treatment options.

[0021] In an embodiment of the invention, the whole-exome sequencing comprises whole- exome sequencing on formalin-fixed paraffin embedded (FFPE) patient tumor tissue. In one aspect, the tumor is a solid tumor. In one aspect, the tumor is a liquid tumor. In one aspect, the tumor is a cancer of one or more tissues selected f om, but not limited to, skin, brain, spinal and other nervous tissue, skeleton, heart, thyroid, lung, liver, spleen, pancreas, kidney, adrenal glands, liver, bladder, gall bladder, breast, muscle, gastrointestinal tract (including without limitation oral cavity, tongue, esophagus, stomach, gut, intestine, colon, rectum), reproductive tract (including without limitation ovary, fallopian tube, uterus, cervix, prostate, penis) and blood cancers including without limitation leukemia, myelomas and lymphoma. In one aspect, the tumor is benign. In one aspect, the tumor is pre-metastatic. In one aspect, the tumor is metastatic.

[0Θ22] In a further embodiment of the invention the tumor comprises gastrointestinal stromal tumors, or skin, for example squamous eel! carcinoma; a hematopoieitic tumor of lymphoid lineage, for example leukemia, acute lymphocytic leukemia, chronic lymphocytic leukemia, B- cell lymphoma (such as diffuse large B cell lymphoma), T-cell lymphoma, Hodgkin's lymphoma, non-Hodgkin's lymphoma, hairy cell lymphoma, or Burkitt's lymphoma; a hematopoieitic tumor of myeloid lineage, including, but not limited to acute myeloid leukemia, chronic myeloid leukemias, myelogenous leukemias, and Imatinib sensitive and refractory chronic myelogenous leukemias, myelodysplastic syndrome, Bortezomib sensitive and refractory multiple myeloma, myeloproliferative disease or promyelocyte leukaemia; thyroid follicular cancer; a tumor of mesenchymal origin, for example fibrosarcoma or rhabdomyosarcoma; a tumour of the central or peripheral nervous system, for example astrocytoma, neuroblastoma, glioma (a High grade glioma) or schwannoma; melanoma (e.g., malignant or metastatic melanoma); seminoma; teratocarcinoma; osteosarcoma; keratoacanthoma; thyroid follicular cancer; Kaposi's sarcoma or E wing's sarcoma.

[0023] In a still further embodiment of the invention the demoting and promoting of somatic variants is based on scoring modifications for known mutations, missense mutations in protein kinase regions, copy number alterations with directionality known to have clinical impact, presence of recurrent alterations in a known database, presence in the pathway of concurrently altered actionable genes in the same sample using curated cancer pathways from a known database, or presence in known cancer pathways, gene sets, or modules identified in a known database.

[0024] The invention also comprehends computer-readable medium comprising codes that, upon execution by one or more processors, implements a herein method of evaluating and ranking genomic alterations in tumor tissue comprising identifying somatic gene variants having clinical or biological relevance for personalized patient tumor treatment options for treating a patient in need of tumor treatment, comprising the steps of: (a) as to tumor tissue of the patient (" atient tumor tissue") that has been subjected to whole exome-sequencing and archival tumor tissue samples that have been subjected to whole-exome sequencing (i) determining concordance of mutations observed in patient tumor tissue that are observed in archival tumor samples and (ii) determining concordance of mutations observed in archival tumor samples that are observed in patient tumor tissue, whereby somatic variants are obtained; (b) generating or accessing a database of genes having therapeutic, prognostic or diagnostic implications for cancer patients or patients having tumors; (c) sorting each somatic variant obtained in step (a) by clinical and biological relevance; (d) linking genes from the database generated or accessed in step (b) with additional biological significant gene data; and (e) demoting variants of uncertain significance, or promoting certain variants of significance; whereby variants of significance are identified and somatic gene alterations having clinical or biological relevance are identified for personalized patient treatment options.

[0025] The invention still, further comprehends computer-readable medium comprising codes that, upon execution by one or more processors, implements a herein method of evaluating and ranking genomic alterations in tumor tissue comprising identifying somatic gene variants having clinical or biological relevance for personalized patient tumor treatment options for treating a patient in need of tumor treatment, comprising the steps of: (a) performing whole-exome sequencing on tumor tissue of the patient ("patient tumor tissue"); (b) performing vvhole-exome sequencing on archival tumor tissue samples; (c) (i) determining concordance of mutations observed in patient tumor tissue that are observed in archival tumor samples and (ii) determining concordance of mutations observed in archival tumor samples that are observed in patient tumor tissue, whereby somatic variants are obtained; (d) generating or accessing a database of genes having therapeutic, prognostic or diagnostic implications for cancer patients; (e) sorting each somatic variant obtained in step (c) by clinical and biological relevance; (f) linking genes from the database generated or accessed in step (d) with additional biological significant gene data; and (g) demoting variants of uncertain significance, or promoting certain variants of significance; whereby variants of significance are identified and somatic gene alterations having clinical or biological relevance are identified for personalized patient treatment options.

[0026] The invention further comprehends a computer system for identifying, evaluating and ranking one or more genes, e.g., in a genome, such as a genome of a eukaryotic organism, the system comprising: a, a memory unit configured to receive and/or store sequence information of the genome; and b. one or more processors alone or in combination programmed to perform a herein method of identifying one or more genes, to thereby identifying a unique gene that has hierarchical importance and display and/or transmit the information on that one or more genes. [0027] The computer system may comprise: (a) a memory unit configured to receive and/or store said nucleic acid sequence; and (b) one or more processors alone or in combination programmed to perform as herein discussed. For example, programmed to: In some embodiments, the nucleic acid sequence in the eukaryotic cell is endogenous to the cell or organism, e.g., eukaryotic genome. In some embodiments, the nucleic acid sequence in the eukaryotic cell is exogenous to the cell or organism, e.g., eukaryotic genome.

[0028] In various aspects, the invention provides a computer-readable medium comprising codes that, upon execution by one or more processors, implements the methods described herein.

[0029] A computer system (or digital device) may be used to receive, transmit, display and/or store results, analyze the results, and/or produce a report of the results and analysis. A computer system may be understood as a logical apparatus that can read instructions from media (e.g., software) and/or network port (e.g., from the internet), which can optionally be connected to a server having fixed media. A computer system may comprise one or more of a CPU, disk drives, input devices such as keyboard and/or mouse, and a display (e.g., a monitor). Data communication, such as transmission of instructions or reports, can be achieved through a communication medium to a server at a local or a remote location. The communication medium can include any means of transmitting and/or receiving data. For example, the communication medium can be a network connection, a wireless connection, or an internet connection. Such a connection can provide for communication over the World Wide Web. It is envisioned that data relating to the present invention can be transmitted over such networks or connections (or any other suitable means for transmitting information, including but not limited to mailing a physical report, such as a print-out) for reception and/or for review by a receiver. The receiver can be but is not limited to an individual, or electronic system (e.g., one or more computers, and/or one or more servers).

[0030] In some embodiments, the computer system comprises one or more processors. Processors may be associated with one or more controllers, calculation units, and/or other units of a computer system, or implanted in firmware as desired. If implemented in software, the routines may be stored in any computer readable memory such as in RAM, ROM, flash memory, a magnetic disk, a laser disk, or other suitable storage medium. Likewise, this software may be delivered to a computing device via any known delivery method including, for example, over a communication channel such as a telephone line, the internet, a wireless connection, etc., or via a transportable medium, such as a computer readable disk, flash drive, etc. The various steps may be implemented as various blocks, operations, tools, modules and techniques which, in turn, may be implemented in hardware, firmware, software, or any combination of hardware, firmware, and/or software. When implemented in hardware, some or all of the blocks, operations, techniques, etc. may be implemented in, for example, a custom integrated circuit (IC), an application specific integrated circuit (ASIC), a field programmable logic array (FPGA), a programmable logic array (PLA), etc.

[0031 J A client-server, relational database architecture can be used in embodiments of the invention. A client-server architecture is a network architecture in which each computer or process on the network is either a client or a server. Server computers are typically powerful computers dedicated to managing disk drives (file servers), printers (print servers), or network traffic (network servers). Client computers include PCs (personal computers) or workstations on which users ran applications, as well as example output devices as disclosed herein. Client computers rely on server computers for resources, such as files, devices, and even processing power. In some embodiments of the invention, the server computer handles all of the database functionality. The client computer can have software that handles all the front-end data management and can also receive data input from users.

[0032] A machine readable medium comprising computer-executable code may take many forms, including but not limited to, a tangible storage medium, a carrier wave medium or physical transmission medium. Non-volatile storage media include, for example, optical or magnetic disks, such as any of the storage devices in any computer(s) or the like, such as may be used to implement the databases, etc. shown in the drawings. Volatile storage media include dynamic memory, such as main memory of such a computer platform. Tangible transmission media include coaxial cables; copper wire and fiber optics, including the wires that comprise a bus within a computer system. Carrier-wave transmission media may take the form of electric or electromagnetic signals, or acoustic or light waves such as those generated during radio frequency (RF) and infrared (IR) data communications. Common forms of com uter-readable media therefore include for example: a floppy disk, a flexible disk, hard disk, magnetic tape, any other magnetic medium, a CD-ROM, DVD or DVD-ROM, any other optical medium, punch cards paper tape, any other physical storage medium with patterns of holes, a RAM, a ROM, a PROM and EPROM, a FLAS H-EPROM, any other memory chip or cartridge, a carrier wave transporting data or instructions, cables or links transporting such a carrier wave, or any other medium from which a computer may read programming code and/or data. Many of these forms of computer readable media may be involved in carrying one or more sequences of one or more instructions to a processor for execution,

[0Θ33] The subject computer-executable code can be executed on any suitable device comprising a processor, including a server, a PC, or a mobile device such as a smartphone or tablet. Any controller or computer optionally includes a monitor, which can be a cathode ray tube ("CRT") display, a flat panel display (e.g., active matrix liquid crystal display, liquid crystal display, etc.), or others. Computer circuitry is often placed in a box, which includes numerous integrated circuit chips, such as a microprocessor, memory, interface circuits, and others. The box also optionally includes a hard disk drive, a floppy disk drive, a high capacity removable drive such as a writeabie CD-ROM, and other common peripheral elements. Inputting devices such as a keyboard, mouse, or touch-sensitve screen, optionally provide for input from a user. The computer can include appropriate software for receiving user instructions, either in the form of user input into a set of parameter fields, e.g., in a GUI, or in the form of preprogrammed instructions, e.g., preprogrammed for a variety of different specific operations.

[0034] An aspect of the invention comprehends a method of performing rapid and robust WES from small amounts of FFPE tumor tissue. A further aspect of the invention comprehends methods of analyzing the W^TES data from small amounts of FFPE tumor tissue to generate analytical output that is equivalent to data from frozen samples. A still further aspect of the invention comprehends clinical interpretation of WES data by using heuristic algorithms to arrive at personalized or individualized tumor or cancer treatments.

[0035] In further aspects, the invention comprehends methods of treating a type of cancer in a patient in need of such treatment comprising administering or not administering a specific treatment in an effective amount or by enrolling or not enrolling said patient in a specific clinical trial to so treat said cancer or improve prognosis of said cancer, comprising analyzing and ranking genes as per the methods of the invention, wherein as a result of the method of the mvention, the specific treatment is not administered or is administered in an effective amount or said patient is enrolled or not enrolled in the specific clinical trial. One can extrapolate this methodology to any cancer or ailment by paralleling aspects of or by analogy to the Example described herein. [0036] Accordingly, it is an object of the invention to not encompass within the invention any previously known product, process of making the product, or method of using the product such that Applicants reserve the right and hereby disclose a disclaimer of any previously known product, process, or method. It is further noted that the invention does not intend to encompass within the scope of the invention any product, process, or making of the product or method of using the product, which does not meet the written description and enablement requirements of the USPTO (35 U.8.C. § 112, first paragraph) or the EPO (Article 83 of the EPC), such that Applicants reserve the right and hereby disclose a disclaimer of any previously described product, process of making the product, or method of using the product.

[0037] It is noted that in this disclosure and particularly in the claims and/or paragraphs, terms such as "comprises", "comprised", "comprising" and the like can have the meaning attributed to it in U.S. Patent law; e.g., they can mean "includes", "included", "including", and the like; and that terms such as "consisting essentially of and "consists essential!)' of" have the meaning ascribed to them in U.S. Patent law, e.g., they allow for elements not explicitly recited, but exclude elements that are found in the prior art. or that affect a basic or novel characteristic of the invention.

[0038] These and other embodiments are disclosed or are obvious from and encompassed by, the following Detailed Description.

BRIEF DESCRIPTION OF THE DRAWINGS

[0Θ39] The novel features of the invention are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present invention will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the invention are utilized, and the accompanying drawings of which:

[0040] Figure l A-C shows FFPE and frozen sample sequencing metrics, (a-c) The percentage of target bases covered at 20 x (a), percentage selected bases (b) and percentage of zero-coverage targets (c) in FFPE (n = 99) and non-FFPE (n = 768) tissue. Additional quality control metrics for all 867 cases are available in Supplementary Table 1 . No statistically significant difference between FFPE and non-FFPE tissue was observed in these three metrics (P > 0.05; two-sided Mann-Whitney U-test). [0041] Figure 2A-2-F shows 2 FFPE and frozen sample data yield comparable alteration data, (a) FFPE and frozen tissue were extracted from identical tumor samples and analyzed for cross-validation of mutations where there was sufficient power to detect the mutation in the validation sample. (b,c) Validation rates for FFPE to frozen (b) and frozen to FFPE (c) binned by allelic fractions demonstrate similar validation and false positive rates between the two groups. (d--f) Copy number profiles derived from exomes of the same tumor in either FFPE or frozen tissue (d) yielded comparable results (r2 = 0.89; P < 0.001, Pearson's correlation) (e). When comparing the FFPE and frozen segment means for all. exons across 1 1 patients (f), the r2 = 0.79 (P < 0.001, Pearson's correlation). CR, copy ratio.

[0042] Figure 3A-G shows PHIAL reveals the long tail of clinically relevant events, (a) PHIAL takes as input somatic alterations and uses heuristics to assign clinical and biological significance to each alteration, (b) PHIAL uses the TARGET database, a curated set of genes that are linked to predictive, prognostic and/or diagnostic clinical actions when somatically altered in cancers. COSMIC, Catalogue of Somatic Mutations in Cancer; CGC, Cancer Gene Census, (c) PHIAL utilizes additional rules to maximize exome data for individuals, including knowledge about kinase domains, copy number directionality and two-hit pathway events, (d) The resulting data were visualized for individual or cohort-level information with this demonstrative PHIAL 'gel'. Each alteration is a point sorted by PHIAL score (top are of highest clinical relevance) and color coded by potential clinical relevance (red), biological relevance (orange), pathway relevance (yellow) or synonymous variants (gray), (e) A PH IAL gel for 51 1 patient exomes spanning six different disease types (n = 258,226 total somatic alterations). The size of the point is proportional to the number of times a given gene arises at that PHIAL score level, (f) This approach highlights the long tail of potentially clinically relevant alterations in TARGET genes (n = 121) that may be present in an individual patient but does not occur sufficiently to be labeled a biological driver across a cohort. The majority of events occur in genes that individually are altered in less than 2% of the overall cohort, (g) New cancer clinical trials with TARGET genes specifically integrated into the study per Cli icalTrials.gov over a 7- year period.

[0043] Figure 4A-B shows clinically relevant findings from individual patients, (a) PHIAL results for 14 patients with a spectrum of malignancies, highlighting nominated clinically actionable alterations in 13 of 14 patients. Asterisks denote patient sequencing data that predated the rapid WES protocol (b) Using the level of evidence schematic, all nominated alterations for patients in this study were manually curated and assigned a level of evidence (Supplementary Table 7).

[0044] Figure 5A-F shows clinical sequencing informs clinical trial enrollment and experimental discovery, (a) The PHIAL output and treatment course for a patient with metastatic lung adenocarcinoma is shown, with the integration of clinical WES occurring during the patient's first-line therapy allowing subsequent clinical trial enrollment, (b) The patient's time- to-relapse data for the three treatment regimens received demonstrate that the clinical response occurred with the CD 4 inhibitor, (c) Computed tomography radiographic imaging demonstrates a small reduction in a representative metastatic focus for the patient on the CDK4 inhibitor trial after two cycles of therapy, consistent with stable disease (measurement is 1 .7 ^x 1.5 cm for baseline mass and 1.3 ^x 1.3 cm for 2-month interval scan of the same mass). Per RECIST criteria, overall tumor reduction was 7.9%. (d) For another patient, PHIA L nominated a JAK3 missense mutation, and given its location in the kinase domain near alterations previously defined as activating, was considered to have inferential evidence (level E) for being clinically actionable, (e) The crystal structure of JAK3 demonstrates that the arginine at residue 870 directly coordinates the phosphate group of the primary activating tyrosine phosphorylation site, (f) To better characterize this alteration, experimental follow-up of this alteration was performed in a Ba/F3 system. Overexpression of the patient's JAK3 mutation was compared to wild -type or a known activating JAK3 mutation (A572V).

[0Θ45] Figure 6A-F shows histology images for studied lung adenocarcinomas, part 1. Low, medium, and high powered images for six lung adenocarcinomas that w^rere included in FFPE and frozen alteration cross-validation studies (A-F).

[0046] Figure 7A-E shows histology images for studied lung adenocarcinomas, part 2. Low, medium, and high powered images for five lung adenocarcinomas that were included in FFPE and frozen alteration cross-validation studies (A.-E).

[0047] Figure 8 shows mean target coverages for FFPE and frozen samples. Mean target coverage for eleven lung adenocarcinomas included in the FFPE and frozen alteration cross- validation analysis. The mean target coverage for all 11 FFPE tumor and germline samples was 1 ,5-2 times that for the corresponding frozen samples. The markedly higher coverage achieved by the FFPE samples increased Applicants' power to detect low allelic traction mutations that Applicants were not powered to detect in the corresponding FF samples.

[0Θ48] Figure 9A-C shows cross-validation results for FFPE and Frozen cases afer "downsampling". Given the uniformly higher mean target coverage achieved for FFPE cases compared to their frozen counterparts. Applicants obtained random subsets of reads from all samples so that all FFPE and FF cases had a maximum coverage of 90X across the exome ("downsam ling"). For sufficiently powered sites in this "downsampled" setting, the FFPE to FF validation rate was 92.6T and the FF to FFPE validation rate was 91.5%, and most false positives occurred at low allelic fractions in both scenarios (A-B). Individual cases had varying amounts of mutations for which there is no power to detect the alteration in the validation sample, but that the validation rate for powered sites is similar across individuals (C).

[0Θ49] Figure lOA-C shows examples of FFPE alterations with insufficient power to validation in the matching frozen case. Demonstrative examples include: low allelic fraction events with insufficient reads in the matched sample (A); no sequencing reads for a particular region in the matched sample (B); or low allelic fraction events with insufficient number of alternate reads in the matched sample.

[0050] Figure 11 shows CRKL amplification in a patient with urothelial carcinoma. A view of the copy radio data for chromosome 22 from patient DFCL l l-104.06 demonstrates a focal amplification that includes CRKL. Given its potential clinical relevance, PHIAL nominated this alteration for manual curation. Additional details about this alteration are available in Supplementary Table 8.

[0051 ] Figure 12 shows a basic format of a PHIAL demo.

[0052] Figure 13 shows a schematic of the PHIAL pipeline with respect to a Lung Ad enocarci noma C ase .

[0053] Figure 14 shows a flowchart of filter, sort and review steps relating to a patient's germline data.

[0054] Figure 15 shows a sample visual of the current CGEC Cancer Genome Report

[0Θ55] Figure 16 shows a screenshot of the somatic analysis window.

[0056] Figure 17 shows a flow chart indicating the steps involved in the PHIAL pipeline.

[0057] Figure 18 shows a schematic representation of the Next-generation sequencing pipeline. [0058] Figure 19 shows a schematic of the existing research pipelines that connect raw genome data to research genomic interpretation.

[0Θ59] Figure 20 shows a schematic of the clinical specific research pipelines that connect raw genome data to research genomic interpretation.

[0060] Figure 21 shows the tier system of classification applied to Actionable, Plausibly Actionable and Theoretical variants under the Investigate Actionability section.

[0061] Figure 22 shows the tier system of classification applied to Actionable, Plausibly Actionable and Theoretical variants with highlights.

[0062] Figure 23 shows a pie chart of 55 prostate cancer whole genomes.

[0063] Figure 24 shows the options of processing high priority genes, priority pathways and other cancer genes under the Investigate Actionability section.

[0Θ64] Figure 25 shows the options of processing variants of uncertain significance and known single nucleotide polymorphisms under the Unknown Variants section.

[0065] Figure 26 show an earlier version of the CGEC Cancer Genome Report.

[0066] Figure 27 shows a screen shot of a sample gene listed under actionable alterations.

[0067] Figure 28 show a screen shot of information sections available under Somatic mutations and indels. The top section of the screen shows information on genes curated. from academic and web based resources and the bottom section of the screen includes findings from heuristics and provides a link to a complete listing of variants uncovered.

[0068] The figures herein are for illustrative purposes only and are not necessarily drawn to scale.

DETAILED DESCRIPTION OF THE INVENTION

[0069] The invention relates to methods, systems, apparatus, e.g., computational and technological methods, systems, apparatus and components thereof and their optimization to arrive at effective clinical analysis of diseases or ailments, e.g., cancer, so that a subject suffering from the disease or ailment and in need of therapeutic intervention for that disease or ailment may be provided with personalized treatment options or considerations. The invention provides for method of ranking and evaluating genomic alterations in the genome of a patient in need of tumor treatment. [0070] As used herein the term "genome" refers to the entirety of an organism's hereditary information. It is encoded either in DNA (e.g., human beings) or RNA (e.g., certain viruses). The genome includes both the genes and the non-coding sequences of the DNA'RNA. Any change in the wild type sequence of the genome that may or may not have phenotypic effects are referred to as "genomic alterations". The term "genomic alterations" encompasses somatic variants or somatic mutations further described herein.

[0071] As used herein, the term "genomic locus" or "locus" (plural loci) is the specific location of a gene or DNA. sequence on a chromosome.

[0072] A "gene" refers to stretches of DNA or RNA that encode a polypeptide or an RNA chain that has functional role to play in an organism and hence is the molecular unit of heredity in living organisms. For the purpose of this invention it may be considered that genes include regions which regulate the production of the gene product, whether or not such regulatory sequences or regulatory elements are adjacent to coding and/or transcribed sequences. Accordingly, a gene includes, but is not necessarily limited to, promoter sequences, terminators, translational regulatory sequences such as ribosome binding sites and internal ribosome entry sites, enhancers, silencers, insulators, boundary elements, replication origins, matrix attachment sites and locus control regions.

[0073] The term "regulatory element" or "regulatory sequence" is intended to include promoters, enhancers, internal liposomal entry sites (IRES), and other expression control elements (e.g., transcription termination signals, such as polyadenylation signals and poly-U sequences). Such regulatory elements are described, for example, in Goeddei, GENE EXPRESSION TECHNOLOGY: METHODS IN ENZYMOLOGY 185, Academic Press, San Diego, Calif. (1990). Regulatory elements include those that direct constitutive expression of a nucleotide sequence in many types of host cell and those that direct expression of the nucleotide sequence only in certain host cells (e.g., tissue-specific regulatory sequences). A tissue-specific promoter may direct expression primarily in a desired tissue of interest, such as muscle, neuron, bone, skin, blood, specific organs (e.g., liver, pancreas), or particular cell types (e.g., lymphocytes). Regulatory elements may also direct expression in a temporal-dependent manner, such as in a cell-cycle dependent or developmental stage-dependent manner, which may or may not also be tissue or cell-type specific. In some embodiments, a vector comprises one or more pol III promoter (e.g., 1, 2, 3, 4, 5, or more pol I promoters), one or more pol II promoters (e.g., 1 , 2, 3, 4, 5, or more pol II promoters), one or more pol I promoters (e.g., 1, 2, 3, 4, 5, or more pol I promoters), or combinations thereof. Examples of pol III promoters include, hut are not limited to, U6 and HI promoters. Examples of pol II promoters include, but are not limited to, the retroviral Rous sarcoma virus (RSV) LTR promoter (optionally with the RSV enhancer), the cytomegalovirus (CMV) promoter (optionally with the CMV enhancer) [see, e.g., Boshart et al, Cell, 41 :521 -530 ( 1985)], the SV40 promoter, the dirr dro folate reductase promoter, the β-actin promoter, the phosphoglycerol kinase (PGK) promoter, and the EFla promoter. Also encompassed by the term "regulatory element" are enhancer elements, such as WPRE; CMV enhancers; the R-U5' segment in LTR ofHTLV-I (Mol. Cell. Biol., Vol. 8(1), p. 466-472, 1988); SV40 enhancer; and the intron sequence between exons 2 and 3 of rabbit β-globin (Proc. Natl. Acad. Sci. USA., Vol. 78(3), p. 1527-31, 1981). It will be appreciated by those skilled in the art that the design of the expression vector can depend on such factors as the choice of the host cell to be transformed, the level of expression desired, etc. A vector can be introduced into host cel ls to thereby produce transcripts, proteins, or peptides, including fusion proteins or peptides, encoded by nucleic acids. A suitable vector as mentioned can be introduced to a cell via one or more methods known in the art, including without limitation, microinjection, electroporation, sonoporation, biolistics, calcium phosphate-mediated transfection, cationic transfection, liposome transfection, dendrimer transfection, heat shock transfection, nucleofection transfection, magnetofection, lipofection, impalefection, optical transfection, proprietary agent- enhanced uptake of nucleic acids, and delivery via liposomes, imtmmoliposomes, virosomes, or artificial virions. In some methods, the vector is introduced into a cell by microinjection. The vector or vectors may be microinjected into the nucleus or the cytoplasm of the cell. In some methods, the vector or vectors may be introduced into a cell by nucleofection. With regards to regulatory sequences, mention is made of U.S. patent application 10/491,026, the contents of which are mcorporated by reference herein in their entirety. With regards to promoters, mention is made of PCT publication WO 2011/028929 and U.S. application 12/511,940, the contents of which are incorporated by reference herein in their entirety.

[0Θ74] The terms "polynucleotide", "nucleotide", "nucleotide sequence", "nucleic acid" and "oligonucleotide" are used interchangeably. They refer to a polymeric form of nucleotides of any length, either deoxyribonucleotides or ribonucleotides, or analogs thereof. Polynucleotides may have any three dimensional structure, and may perform any function, known or unknown. The following are non-limiting examples of polynucleotides: coding or non-coding regions of a gene or gene fragment, loci (locus) defined from linkage analysis, exons, mtrons, messenger RNA (mRNA), transfer RNA, ribosomai RNA, short interfering RNA (siRNA), short-hairpin RNA (shRNA), micro-RNA (miRNA), ribozymes, cDNA, recombinant polynucleotides, branched polynucleotides, plasmids, vectors, isolated DNA of any sequence, isolated RNA of any sequence, nucleic acid probes, and primers. The term also encompasses nucfeic-acid-like structures with synthetic backbones, see, e.g., Eckstein, 1991; Baserga et al., 1992; Milligan, 1993; WO 97/0321 1; WO 96/39154; Mata, 1997; Strauss-Soukup, 1997; and Samstag, 1996. A polynucleotide may comprise one or more modified nucleotides, such as methylated nucleotides and nucleotide analogs. If present, modifications to the nucleotide structure may be imparted before or after assembly of the polymer. The sequence of nucleotides may be interrupted by non-nucleotide components. A polynucleotide may be further modified after polymerization, such as by conjugation with a labeling component,

[0Θ75] As used herein, "expression of a genomic locus" or "gene expression" is the process by which information from a gene is used in the synthesis of a functional gene product. The products of gene expression are often proteins, but in non-protein coding genes such as rRNA genes or tRNA genes, the product is functional RNA. The process of gene expression is used by all known life - eukaryotes (including multicellular organisms), prokaryotes (bacteria and archaea) and viruses to generate functional products to survive. As used herein "expression" of a gene or nucleic acid encompasses not only cellular gene expression, but also the transcription and translation of nucleic acid(s) in cloning systems and in any other context. As used herein, "expression" also refers to the process by which a polynucleotide is transcribed from a DNA template (such as into and mRNA or other RNA transcript) and/or the process by which a transcribed mRNA is subsequently translated into peptides, polypeptides, or proteins. Transcripts and encoded polypeptides may be collectively referred to as "gene product." if the polynucleotide is derived from genomic DNA, expression may include splicing of the mRN A in a eukaryotic cell.

[0Θ76] As used herein the term "wild type" is a term of the art understood by skilled persons and means the typical form of an organism, strain, gene or characteristic as it occurs in nature as distinguished from mutant or variant forms. The terms "non-naturally occurring", "recombinant" or "engineered" are used interchangeably and indicate the involvement of the hand of man. The terms, when referring to nucleic acid molecules or polypeptides mean that the nucleic acid molecule or the polypeptide is at least substantially free from at least one other component with which they are naturally associated in nature and as found in nature.

[0077] As used herein the term "variant" should be taken to mean the exhibition of qualities that have a pattern that deviates from what occurs in nature. The term also encompasses exhibition of qualities that has a pattern that deviates from the accepted wild type form. As used herein the term "mutation" refers to a change of the nucleotide sequence of the genome of an organism, virus, or extrachromosomal genetic element. In aspects of the invention the terms "variant" and "mutation" may be used interchangeably. Small-scale mutations, such as those affecting a smal l gene in one or a few nucleotides, include:

[0078] Point mutations, often caused by chemicals or malfunction of D^'NA replication, exchange a single nucleotide for another. These changes are classified as transitions or transversa ons. Most common is the transition that exchanges a purine for a purine (A > G) or a pyrimidine for a pyiimidine, (C *→ T). A transition can be caused by nitrous acid, base mis- pairing, or mutagenic base analogs such as 5-bromo-2-deoxyuridine (BrdU). Less common is a transversion, which exchanges a purine for a pyrimidine or a pyrimidine for a purine (C/T <→ A/G). An example of a transversion is adenine (A) being converted into a cytosine (C). A point mutation can be reversed by another point mutation, in which the nucleotide is changed back to its original state (true reversion) or by second-site reversion (a complementary mutation elsewhere that results in regained gene functionality). Point mutations that occur within the protein coding region of a gene may be classified into three kinds, depending upon what the erroneous codon codes for: Silent mutations: which code for the same (or a sufficiently similar) amino acid. Missense mutations: which code for a different amino acid. Nonsense mutations: which code for a stop and can truncate the protein.

100791 Insertions add one or more extra nucleotides into the DNA. They are usually caused by transposable elements, or errors during replication of repeating elements (e.g., AT repeats Yang et aL Genome Res. 2004. 14: 517-527). Insertions in the coding region of a gene may after splicing of the mRNA (splice site mutation), or cause a shift in the reading frame (frameshift), both of which can significantly alter the gene product. Insertions can be reversed by excision of the transposable element.

[0080] Deletions remove one or more nucleotides from the DNA. Like insertions, these mutations can alter the reading frame of the gene. They are generally irreversible: though exact!)' the same sequence might theoretically be restored by an insertion, transposable elements able to revert a very short deletion (say 1-2 bases) in any location are either highly unlikely to exist or do not exist at ail Note that a deletion is not the exact opposite of an insertion: the former is quite random while the latter consists of a specific sequence inserting at locations that are not entirely random or even quite narrowly defined.

[0081] Large-scale mutations in chromosomal structure, include: Amplifications (or gene duplications) leading to multiple copies of all chromosomal regions, increasing the dosage of the genes located within them.

[0082] Deletions of large chromosomal regions, leading to loss of the genes within those regions.

[0083] Mutations whose effect is to juxtapose previously separate pieces of D A, potentially bringing together separate genes to form functionally distinct fusion genes (e.g., ber- abl). These include: Chromosomal translocations: interchange of genetic parts from nonhomologous chromosomes.

[0084] interstitial deletions: an mtra-chromosornal deletion that removes a segment of DNA from a single chromosome, thereby apposing previously distant genes. For example, cells isolated from a human astrocytoma, a type of brain tumor, were found to have a chromosomal deletion removing sequences between the "fused in glioblastoma" (fig) gene and the receptor tyrosine kinase "ros", producing a fusion protein (FIG-ROS). The abnormal FIG-RGS fusion protein has constitutively active kinase activity that causes oncogenic transformation (a transformation from normal cells to cancer cells),

[0085] Chromosomal in versions: reversing the orientation of a chromosomal segment.

[0086] Loss of heterozygosity : loss of one allele, either by a deletion or recombination event, in an organism that previously had two different alleles.

[0087] As used herein the term "somatic" refers to aspects of the body that do not relate to the germ line. For example, somatic cells are cells of the body that are not germ line cells that give rise to reproductive cells or gametes. "Somatic mutations" or "somatic variants", the terms may be used interchangeably, are changes to the genetics of a multicellular organism which are not passed on to its offspring through the germline. Many cancers are somatic mutations. Aspects of the invention may certainly extend to analysis of germline mutations or variants as well. [0088] The terms "polypeptide", "peptide" and "protein" are used interchangeably herein to refer to polymers of amino acids of any length. The polymer may be linear or branched, it may comprise modified amino acids, and it may be interrupted by non amino acids. The terms also encompass an amino acid polymer that has been modified; for example, disulfide bond formation, glycosylation, lipidation, acetylation, phosphorylation, or any other manipulation, such as conjugation with a labeling component. As used herein the term "amino acid" includes natural and/or unnatural or synthetic amino acids, including glycine and both the D or L optical isomers, and amino acid analogs and peptidomimetics.

[0089] As used herein, the term "domain" or "protein domain" refers to a part of a protein sequence that may exist and function independently of the rest of the protein ch ain.

[0090] As used herein, the term "tumor" is commonly used as a synonym for a neoplasm (a solid or fluid-filled (cystic) lesion, or a hematopoeitic neoplasm such as a leukemia or lymphoma or liquid tumor, that may or may not be formed by an abnormal growth of neoplastic cells) that appears enlarged in size. Tumor is not generally synonymous with cancer as while cancer is by definition an uncontrolled division of abnormal cells, a tumor can be benign, pre -malignant, or malignant, or can represent a lesion without any cancerous potential whatsoever. Depending on the context of use, the terms tumor and cancer may be used interchangeably in this application.

[0091] As used herein the term "cancer" refers to one or more of family of diseases caused by an uncontrolled division of abnormal cells in a part of the body. It may also refer to the malignant growth or tumor resulting from such a division of cells. Cancer is a proliferative disorder.

[0092] Cancer may affect several organisms, including human beings. Forms of cancer have been identified in plants, domestic animals (cats and dogs) and wild animals. Examples of wild animals affected by cancer include but are not limited to Tasmanian devils, sharks, beluga whales, brown bullhead catfish, English sole, dusky dolphin, Burmeister's porpoise and green sea turtles. Aspects of the invention may encompass evaluation and ranking of genes in other non-human organisms.

[0093] As used herein, the term "tumor tissue" refers to biological tissue samples derived from tumor specimens, including but not limited to snap-frozen or fresh-frozen (FF) tissue samples, FFPE and matching blood products. The tumor specimen may belong to an organism, e.g., human, dog, cat etc. Preferably, the tumor tissue is obtained from a human or patient in need of tumor treatment. When a patient undergoes a biopsy or surgical excision of tissue for medical diagnosis and/or guidance in therapy, the removed tissue is sent to the pathology department, where it is processed for microscopic evaluation. Once the diagnostic process is completed, this material becomes part of the patient's pennanent medical record. Diagnostic slides and blocks may be stored by pathology departments or tissue archival establishments which serve as the custodians of diagnostic archival formalin fixed paraffin embedded tissues and corresponding hematoxylin and eosin stained slides. Tumor tissue samples obtained from the patient on previous visits or different patients with, a similar tumor condition or cancer obtained from a tissue archive is referred to as "archival tumor tissue".

[0094] The terms "treat," treating," "treatment," and the like refer to reducing or ameliorating a disease or ailment or symptoms associated therewith. In a preferred embodiment, the disease is cancer. It will be appreciated that, although not precluded, treating cancer or the risk of developing cancer does not require that the disease or the risk be completely eliminated. Aspects of treating cancer relate to providing a patient with a tumor treatment.

[0095] The term "concordance" as used herein refers to the probability that a pair of individuals will both have a certain characteristic, given that one of the pair has the characteristic. Detennining the concordance of mutations refers to the probability that a certain mutation is present in one individual when compared to another individual who may be suffering from the same or different disease condition.

[0096] Aspects of the invention relate to promoting and demoting certain variants of significance or uncertain significance. This analysis is based on ranking identified genes higher or lower based on whether the gene displays characteristics of interest. The characteristics of interest may include but are not limited to whether the one or more mutations present in the gene are known or have been previously identified, whether the one or more mutations present in the genes are missense mutations in protein kinase regions or domains, whether the genes have altered copy numbers and if those copy number alterations have a directionality known to have clinical impact or significance, whether recurrent alterations are present in a known database, whether the gene is present in the pathway of concurrently altered actionable genes in the same sample using curated cancer pathways from a known database, or whether the gene is present in known cancer pathways, gene sets, or modules identified in a known database. This ranking of genes based on their possession of characteristics listed or on other relevant characteristics that may be identified may be represented in a visual format with genes ranked higher being represented by color coded dots (say red dots) placed higher in the panel while other genes with lower ranking are place lower in the panel (say orange, yellow or grey dots) as indicated in Figure 4, In arriving at personalized tumor treatment options for a patient it is important to consider the genes placed higher in the panel and to determine all aspects of their structure and function as well as consider other genes which may be present in linked pathways.

[0097] A clinical trial is a rigorously controlled test of a new drug or a new invasive medical device on human subjects. Clinical trials generate safety and efficacy data (or more specifically, information about adverse drug reactions and adverse effects of other treatments) for health interventions (e.g., drugs, diagnostics, devices, therapy protocols). They are conducted only after satisfactory information has been gathered on the quality of the nonclinical safety, and health authority/ethics committee approval is granted in the country where approval of the drug or device is sought. In the United States clinical trials are conducted under the direction of the FDA before being made available for general clinical use. Clinical trials involving new drugs are commonly classified into four phases. Each phase of the drug approval process is treated as a separate clinical trial. The drag-development process will normally proceed through all four phases over many years. If the drug successfully passes through Phases 0, 1 , 2, and 3, it will usually be approved by the national regulatory authority for use in the general population.

Phase 0: Pharmacodynamics and Pharmacokinetics

Phase 1 : Screening for safety

Phase 2: Establishing the efficacy of the drug, usually against a placebo

Phase 3: Final confirmation of safety and efficacy

Phase 4: Sentry studies during sales

Each phase has a different purpose and helps scientists answer a different question:

Phase 0 trials are the first-in-human trials. Single subtherapeutic doses of the study drug are given to a small number of subjects (10 to 15) to gather preliminary data on the agent's pharmacodynamics (what the drug does to the body) and pharmacokinetics (what the body does to the drugs).

[0098] In Phase 1 trials, researchers test an experimental dr g or treatment in a small group of people (20-80) for the first time to evaluate its safety, determine a safe dosage range, and identity side effects. In Phase 2 trials, the experimental treatment is given to a larger group of people (100-300) to see if it is effective and to further evaluate its safety. In Phase 3 trials, the treatment is given to large groups of people (1,000-3,000) to confirm its effectiveness, monitor side effects, compare it to commonly used treatments, and collect information that will allow it to be used safely. In Phase 4 trials, postmarketing studies delineate additional information, including the treatment's risks, benefits, and optimal use. Before pharmaceutical companies start clinical trials on a drug, the)' conduct extensive preclinical studies. Information on clinical trials being conducted may be accessed at the website clinicaltrials.gov which is a registry and results database of publicly and privately supported clinical studies of human participants conducted around the world.

[0099] Cancer research is the intense scientific effort to understand disease processes and discover possible therapies. Research about cancer causes focuses on the following issues: a) Agents (e.g., viruses) and events (e.g., mutations) which cause or facilitate genetic changes in cells destined to become cancer; b) The precise nature of the genetic damage, and the genes which are affected by it; and c) The consequences of those genetic changes on the biology of the cell, both in generating the defining properties of a cancer cell, and in facilitating additional genetic events which lead to further progression of the cancer. Targeted cancer therapies interfere with cancer cell division (proliferation) and spread in different ways. Many of these therapies focus on proteins that are involved in cell signaling pathways, which form a complex communication system that governs basic cellular functions and activities, such as cell division, cell movement, cell responses to specific external stimuli, and even cell death. By blocking signals that tell cancer cells to grow and divide uncontrollably, targeted cancer therapies can help stop cancer progression and may induce cancer cell death through a process known as apoptosis. Other targeted therapies can cause cancer cell death directly, by specifically inducing apoptosis, or indirectly, by stimulating the immune system to recognize and destroy cancer cells and/or by delivering toxic substances directly to the cancer cells. The development of any cancer therapy, therefore, requires the identification of good targets and advances in next generation sequencing combined with bioinformati.es and computational approaches may help analyze the abundance of scientific information available on genes in a clinically relevant time line.

[00100 J Exome sequencing (also known as targeted exome capture) is an efficient strategy to selectively sequence the coding regions of the genome as a cheaper but still effective alternative to whole genome sequencing. Exons are short, functionally important sequences of DNA. which represent the regions in genes that are translated into protein and the untranslated region (UTR) flanking them. UTRs are usually not included in exome studies. In the human genome there are about 180,000 exons: these constitute about 1% of the human genome, which translates to about 30 megabases (Mb) in length. It is estimated that the protein coding regions of the human genome constitute about 85% of the disease-causing mutations.

[00101 J Whole Exome Sequencing (WES) : Genome Wide Association Studies (GWAS) using SNP markers has been widely used for discovery of genetic risk factors for human disease. However, this method will only reveal risk factors that are common in the population. Instead, a more comprehensive method such as whole-genome sequencing would reveal all de-novo and low frequency alleles that contribute to genetic risk for disease. At this time, whole genome sequencing is too expensive to perform for large sample sizes, however aspects of the invention also comprehend analysis via whole-genome sequencing. WES, as referred to herein, was a technique developed to fill the niche between GWAS and whole-genome sequencing; capture and sequencing of only the exons in the genome. This comprises roughly 2-3% of the genome. The approach reduces the sequencing needed by 97%, yet retains the most likely sources of genetic disease risk. The method is a cost-effective way to study families affected by inherited disease or a large number of family trios. Custom panels can be synthesized that cover a limited gene set or for model organisms. The method is well established; three major companies produce commercial products for whole-exome capture and sequencing. These are Roche/NimbleGen (SeqCap EZ), Agilent Technologies (Sure-Select) and Hlumina (TruSeq Exome Enrichment).

[0Θ102] All methods are variants on the following strategy: DNA is sheared and then ligated to adapters that enable sequencing on the Illumina platform. The library is amplified by PGR and then hybridized to a pool of biotinylated oligos specific for exons ("baits"). The size of the genome region captured is generally 30-60 megabase. Strepavidm magnetic beads are used to separate genomic DNA-bait hybrids; this library fraction should be enriched for exons (~3% of genome). A second round of PGR. is used to amplify the library to sufficient levels to sequence. The enriched library is checked by real-time PGR to determine the exon enrichment was successful. Then, the library is sequenced with paired end reads (lOOnt x 2 on the HiSeq 2000) to achieve a depth of 20-3()x per base. Genomic Library Preparation: Three steps are required for preparation of an exon enriched gDNA library for massively parallel sequencing; (1) a library of genomic DNA is created, (2) the library is enriched for exon targets, and (3) the library quality and enrichment is verified. Illumina sequencing performs best when a DNA strands are <500 bp in size, thus, high molecular weight genomic DNA must be sheared. Applicants use the Covaris Acoustic Disruptor (E210), to achieve a narrow 200-300nt size distribution of chromosomal DNA. The Covaris instrument has major advantages over standard shearing techniques: it can be used with low quantities of DNA (250ng-5 .ug), sample recovery is higher than nebulization, and the samples are sheared in individual tubes, reducing the risk of cross-contamination by sonication probe. DNA derived from blood, saliva or tissue may be used; samples may be processed in a 96-wel.l format. Each molecule in the DNA library must contain two specific sequences at its ends to be sequenced on the Illumina platform. These sequences are introduced by the following methods: after shearing the sequence library contains ends with 5 ' and 3 ' overhangs, these are filled-in using T4 polymerase and T4 polynucleotide kinase resulting in blunt-ended DNA molecules. Then a deoxyadenosine (dA) 5 ^' tail is added to DNA strands using the Klenow fragment (exo~). Double stranded DN A adapters with 3 ^' thymidine overhangs are iigated to the dA tailed library using T4 ligase; the adapters contain the sequences needed for binding to the sequencing flow cell and sequencing primer binding sites. Sequencing adapter- dimers wastes reagents; to exclude adapter-dimers from the sequencing pool, the library must be size selected by agarose gel electrophoresis or with SPRI beads (Beckman Coultier Ampure XP). The DNA library is then enriched for sequences with 5 ' and 3 ^' adapters by PCJR with primers complementary to the adapter sequences (ligation-mediated PCR, LM-PCR).

[00103] Capturing Library Strands Containing Exons: Genomic DNA libraries prepared as above contain ~2-3% exon derived sequences. Changes in amino acid sequence are often the cause of phenotypic variation. Thus, exon sequencing is cost effective compared to whole genome sequencing because it is likely to yield informative variants with a fraction of sequencing effort. Three commercial platforms are currently available for exon sequence enrichment from DNA libraries: Agilent Technologies' "Sure Select", Roche NimbleGen's "Seq Cap EZ" and Illumina's "TruSeq Exome Enrichment". Both methods involve the following: a tiling exon oligonucleotide microarray is synthesized and used to create a pool of biotinyiated nucleic acids or "baits". The capture reagent baits may be RNA (Agilent Technologies) or DNA (Roche Nimbi eGen) and may vary in length from 60 to 120 nt. Baits are incubated with adapter- ligated DNA libraries in solution over 24-72 hours, allowing the hybridization of bait to target sequences. The bait-target hybrids are captured by streptavidin magnetic microbeads, and then beads are washed to remove non-specifically bound DNA and eluted. A secondary LM-PCR is performed to generate sufficient DNA for sequencing.

[0Θ104] Enriched libraries are then validated by Agilent BioAnalyzer for size distribution. Before the library is sequenced, we perform a real-time SYBR Green PGR using 6 exon-intron pairs to compare equal masses of whole-genome and exon-captured libraries. An exon-capture experiment is considered successful if all six exons are enriched and ail six mtrons are depleted; this proxy method allows detection of failed capture experiments before sequencing is initiated. Samples are then ready for sequencing on the I!Iumina HiSeq 2000. As of March 2012, sufficient coverage for SNP calling is achieved by sequencing three samples per lane.

[00105] The term "prognostic" refers to predicting the likely outcome of a disease; of or relating to a prognosis. The term "therapeutic" refers to relating to the treatment of disease or disorders by remedial agents or methods. The term "diagnostic" refers to identifying the nature or cause of a disease, or use in diagnosis,

[00106] As used herein, the term "database" refers to an organized collection of data. The term may encompass the data itself and the supporting data structures. Databases are created to operate large quantities of information by inputting, storing, retrieving, and managing that information. Databases are set up so that one set of software programs may provide all users with access to all the data. The term may also encompass the concept of metadatabases, a database of databases, rather than any one integration project or technology. Databases as used herein include but are not limited to primary nucleotide sequence databases, genome databases, protein sequence databases, proteomics databases, protein structure databases, protein model databases, RNA databases, Carbohydrate structure databases, Protein -protem interactions, Signal transduction pathway databases, Metabolic pathway databases, Microarray databases, Exosomal databases, Mathematical model databases, PCR / real time PGR primer databases, Specialized databases (such as those on antibodies), Taxonomic databases and Wild-style databases. In a preferred aspect of the invention, a database of genes is generated or accessed.

[00107] in general, the term "algorithms" refer to an effective method expressed as a finite list of well-defined instructions for calculating one or more functions of interest. Algorithms may be expressed in several kinds of notation, including but not limited to programming languages, flow charts, control tables, natural languages, mathematical formula and pseudocode. In a preferred embodiment, the algorithm may be expressed in a programming language that expresses the algorithm in a form that may be executed by a computer or a computer system.

[0Θ108] Aspects of the invention relate to the utilization of several bioinformatics and computational tools and databases, which include but are not limited to PHIAL, TARGET, ABSOLUTE, Picard, Firehose, GenePattem, ContEst, R statistical package, MuTect, Idelocator, Oncotator, dRanger, RefSeq, Cancer Gene Census (CGC), MSigDB, MutSigl .O, MutSigl .5, MutSig2.0, MutSigCV, MutSigS2N and C SMIC.

[00109] A key aspect of the invention relates to PHIAL (Precision Heuristics for Interpreting the Alteration Landscape), a heuristic algorithm for clinical interpretation of cancer genome sequencing data. Sequencing data may generate hundreds to thousands of alterations per patient, including mutations, short insertions and deletions, and copy number alterations. The purpose of PHIAL is to utilize a rule-based approach to rank the alterations by clinical and biological significance, so that the most clinically relevant alterations can be rapidly identified for clinical review. PHIAL utilizes the TARGET database, which is a set of curated genes that, when altered somatically, are linked to clinical actions.

[00110] As referred to herein, TARGET (tumor alterations relevant for genomics-driven therapy) is a database of genes that, when somatically altered in cancer, are directly linked to a clinical action. TARGET genes may be predictive of response or resistance to a therapy, prognostic, and/or diagnostic. TARGET is intended to be a community resource for translational oncology. To maintain relevance and keep pace with new preclinical and clinical discoveries, it is updated quarterly.

[00111] As referred to herein, MutSig stands for "Mutation Significance". MutSig analyzes lists of mutations discovered in DNA sequencing, to identify genes that were mutated more often than expected by chance given background mutation processes, as further described in Lawrence, M. et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 499, 214-218 (2013), incorporated by reference herein in its entirety. The input data to MutSig is lists of mutations (and indels) from a set of samples (patients) that were subjected to DNA sequencing, as well as information about how much territory was covered in the sequencing. MutSig was originally developed for analyzing somatic mutations, but it has also been useful in analyzing germline mutations. MutSig builds a model of the background mutation processes that were at work during formation of the tumors, and it analyzes the mutations of each gene to identify genes that were mutated more often than expected by chance, given the background model.

[00112] A critical component of MutSigCV is the background model for mutations, the probability that a base is mutated by chance. Patients being analyzed do not all have the same background mutation rate, or the same spectrum of mutations. Similarly, not ail regions of the genome (or exome) have the same background mutation patterns. MutSig has been evolving since the early days of clinical sequencing, and several versions have been in use:

[00113] MutSig 1.0 assumed a constant background mutation rate (BMR) across the genome. MutSig 1.5 implemented a rudimentary estimate of per-gene background mutation rates from analyzing the silent (synonymous) mutations of each gene and the rough expression level of the gene. MutSig2.0, although named similar!)' to the above versions, is actually a rather different animal. While the versions listed above consider the * abundance* of mutations above background, this part of MutSig looks at two additional independent signals of positive selection in genes: the * clustering* of mutations in hotspots, and the functional impact of the mutations, which can be estimated in a number of ways (PolyPhen, SIFT, CHASM, Mutation Assessor, etc.), or even simply from the * conservation* of the sites— that is, how conserved they were during vertebrate evolution. These two signals are then combined with each other and with the results of MutSig 1.5 to yield a final measure of significance that takes all three signals (Abundance, Clustering, and Conservation) into account. MutSigS2N was a rudimentary precursor of MutSigCV, used in a few interim projects before MutSigCV was developed.

[00114] MutSigCV is a current version of the algorithm. The "CV" stands for "covariates". MutSigCV starts from the observation that the data is very sparse, and that there are usually too few silent mutations in a gene for its BMR to be estimated with any confidence. MutSigCV improves the BMR. estimation by pooling data from 'neighbor' genes in covariate space. These neighbor genes are chosen on the basis of having similar genomic properties to the central gene in question: properties such as DNA replication time, chromatin state (open/closed), and general level of transcription activity (e.g., high!)' transcribed vs. not transcribed at all). These genomic parameters have been observed to strongly con-elate (co-vary) with background mutation rate. For instance, genes that replicate early in S-phase tend to have much lower mutation rates than late-replicating genes. Genes that are highly transcribed also tend to have lower mutation rates than unexpressed genes, due in part to the effects of transcription-coupled repair (TCR). Genes in closed chromatin (as measured by HiC or ChipSeq) have higher mutation rates than genes in open chromatin, incorporating these covariates into the background model substantially reduces the number of false-positive findings. In summary, MutSigCV creates a comprehensive catalogue of all the genes responsible for the initiation and progression of cancer involved the sequencing of matched tumor-normal samples followed by mathematical analysis to identify those genes in which mutations occur more frequent!)' than expected by random chance. However, as the sample size increases, the list of putatively significant genes produced by current analytical methods burgeons into the hundreds. The list includes many implausible genes (such as those encoding olfactory receptors and the muscle protein titin), suggesting extensive false positive findings that overshadow true driver events. Lawrence et ah, 2013, Nature 499, 214-218 show that this problem stems largely from mutational heterogeneity and provide a novel analytical methodology, MutSigCV, for resolving the problem. By incorporating mutational heterogeneity into the analyses, MutSigCV eliminated most of the apparent artefactual findings and enable the identification of genes truly associated with cancer,

[00115] Whole-ex ome capture libraries were constructed and sequenced on Illumina HiSeq flowcells to an average coverage of 118X. Whole-genome sequencing was done with the Illumina GA-II or Illumina HiSeq sequencer, achieving an average of about 30X coverage depth. Reads w^rere aligned to the reference human genome build hgl9 using an implementation of the Burrows- Wheeler Aligner, and a BAM file was produced for each tumor and normal sample using the Picard pipeline (Chapman, M.A. et al. Nature 471 , 467-472 (201 1 )). The Firehose pipeline was used to manage input and output files and submit analyses for execution. The MuTect (Cibulskis, K. et al. Nature Biotechnol, 31, 213-219 (2013)) and hidelocator algorithms were used to identify somatic single-nucleotide variants and short somatic insertions and deletions, respectively. Mutation spectra were analyzed using NMF. Significantly mutated genes w^rere identified using MutSigCV, which estimates the background mutation rate for each gene-patient-category combination based on the observed silent mutations in the gene and non- coding mutations in the surrounding regions. Because in most cases these data are too sparse to obtain accurate estimates, accuracy was increased by pooling data from other genes with similar properties (for example, replication time, expression level). Significance levels (P values) were determined by testing whether the observed mutations in a gene significantly exceeded the expected counts based on the background model. False-discovery rates (q values) were then calculated, and genes with q<0.1 were reported as significantly mutated.

[0ΘΙΙ6] As referred to herein, the Molecular Signatures Database (MSigDB), is a collection of annotated gene sets for use wit GSEA softwares. It is further described in Subramanian, A., Tamayo, P., Mootha, V.K., Mukherjee, S., Ebert, B.L., et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome -wide expression profiles. Proceedings of the National Academy of Sciences of the United States of America 102, 15545-15550 (2005). MSigDB gene sets are divided into 7 major collections: 1 . positional gene sets for each human chromosome and cytogenetic band. 2. curated gene sets from online pathway databases, publications in PubMed, and knowledge of domain experts. 3. motif gene sets based on conserved cis-regulatory motifs from a comparative analysis of the human, mouse, rat, and dog genomes. 4. computational gene sets defined by mining large collections of cancer-oriented microarray data. 5. GO gene sets consist of genes annotated by the same GO terms. 6. oncogenic signatures defined directly from microarray gene expression data from cancer gene perturbations. 7. immunologic signatures defined directly from microarray gene expression data from immunologic studies.

[00117] As referred to herein, ABSOLUTE can detect subclonal heterogeneity and somatic homozygosity and it can calculate statistical sensitivity for detection of specific aberrations. In other words, ABSOLUTE can estimate purity/ploidy, and from that compute absolute copy- number and mutation multiplicities. When DNA is extracted from an admixed population of cancer and normal cells, the information on absolute copy number per cancer ceil is lost in the mixing. The purpose of ABSOLUTE is to re-extract these data from the mixed DNA population. This process begins by generation of segmented copy number data, which is input to the ABSOLUTE algorithm together with pre-computed models of recurrent cancer karyotypes and, optionally, allelic fraction values for somatic point mutations. The output of ABSOLUTE then provides re-extracted information on the absolute cellular copy number of local DNA. segments and, for point mutations, the number of mutated alleles.

[0Θ118] ABSOLUTE was used to analyze exome sequencing data from 214 ovarian carcinoma tumor-normal pairs and infer absolute allelic copy-number profiles from 3,155 diverse cancer specimens, revealing that genome-doubling events are common in human cancer, likely occur in cells that are already aneuploid, and influence pathways of tumor progression (for example, with recessive inactivafion of NF1 being less common after genome doubling) (Carter et al., 2012, Nat. Biotechnol. 30, 413-421). ABSOLUTE may facilitate the design of clinical sequencing studies and studies of cancer genome evolution and intra-tumor heterogeneity.

[00119] An overview of tumor DNA analysis using ABSOLUTE is presented in Figure 1 of Carter et al, 2012, Nat. Biotechnol. 30, 413-421. A constant mass of DNA is extracted from a heterogeneous cell population consisting of cancer and normal cel ls. This DNA is profiled using either microarray or massively parallel sequencing technology, giving a genome -wide profile of DNA concentrations. The copy ratios for both homologous chromosomes are shown for each genomic segment with locally constant copy number. A color axis indicates distance between low (blue) and high (red) homologue concentration; segments where these are similar (allelic balance) are purple. Copy ratios were binned at 0.04 resolution (y axis); the length of each block corresponds to the (hapioid) genomic fraction (x axis) of each corresponding segment in b. Several discrete SCNA peaks are visible, each corresponding either to an (unknown) integer copy state in the somatic clone or to a subclonal alteration. To aid in the interpretation of potentially ambiguous data, ABSOLUTE uses pre-compute statistical models of recurrence cancer karyotypes. Optionally, if somatic point mutation data are available (from sequencing of the DN A), then the allelic fractions (fraction of sequencing reads bearing the nonreference allele) of these mutations may be used help to interpret the DNA concentrations. Candidate solutions lie on the indicated grid of b = 2(1 - a)/D and δτ = α/D (equation (1)). The log-likelihood (score) of each solution in terms of the SCNA fit of the observed copy ratios to integer absolute copy numbers and plausibility of the proposed karyotype. The highest-scoring solution is identified by the combination of SCNA-fit and karyotype log-likelihood values. This interpretation implies subclonal gain of chromosome 2. The SCNA score alone cannot distinguish between this and an additional solution but the overall SCNA-fit score is equivalent to that of the first solution.

[00120] The inference framework used in ABSOLUTE may be described as follows (Carter et al., 2012, Nat. Biotechnol. 30, 413-421). Suppose a cancer-tissue sample consists of a mixture of a proportion a of cancer cells (assumed to be monogenomic that is, with homogenous SCNAs in the cancer ceils) and a proportion (1 - a) of contaminating normal (diploid) cells. For each locus x in the genome, let q(x) denote the integer copy number of the locus in the cancer cells. Let τ denote the mean ploidy of the cancer-cell fraction, defined as the average value of q(x) across the genome. In the mixed cancer sample, the average absolute copy number of locus x is a q(x) + 2(1 - a) and the average ploidy (D) is ατ + 2(1 - a), measured in units of hapioid genomes. The relative copy number (R) of locus x is therefore: .

[0Θ12Ι] Because q(x) takes integer values, R(x) takes discrete values. The smallest possible value is (2(1 - a)/D), which occurs at homozygously deleted loci and corresponds to the fraction of DNA from normal cells. The spacing between values (ot/D) corresponds to the concentration ratio of alleles present at one copy per cancer cell and zero copies per normal cell. Notably, if a cancer sample is not strictly clonal, copy-number alterations occurring in substantial subclonal fractions will appear as outliers from this pattern. Similar considerations have formed the basis for algorithms to infer purity and ploidy using allelic copy-ratios derived from single- nucleotide polymorphisms (SNP) microarrays.

[00122] Absolute cop)' inference may be extended to encompass somatic point mutations as follows: Here, sq represents the multiplicity of the point mutation, in integer values per cancer cell (which cannot exceed q(x)), and Ds = aq(x) + 2(1 - a). The values of F(x) correspond to the expected fraction of sequencing reads that support the mutation, which depend on the sample purity and absolute somatic copy number at the mutant locus, q(x).

[00123] The ABSOLUTE algorithm examines possible mappings from relative to integer copy numbers by jointly optimizing the two parameters a and τ In many cases, several such mappings are possible, corresponding to multiple optima.

[00124] To help resolve ambiguous cases, recurrent cancer-karyotype models based on large data sets were used to identify the simplest (that is, most common) karyotype that can adequately explain the data. This method favors simpler solutions, while preserving the flexibility to identify unexpected karyotypes given sufficient evidence from the copy profile. Indeed, several unusual karyotypes, including near-hap oid (<1.2n) and hyperaneuploid (>6n) genomes, were identified using ABSOLUTE.

[00125] ABSOLUTE applied: Clonal evolution is a key feature of cancer progression and relapse. Intratumoral heterogeneity was in 149 chronic lymphocytic leukemia (CLL) cases by integrating whole-exome sequence and copy number to measure the fraction of cancer cells harboring each somatic mutation (Landau et al., Cell 152, 714—726, February 14, 2013). Driver mutations were identified as predominantly clonal (e.g., MYD88, trisomy 12, and del(13q)) or subclonal (e.g., SF3B1 and TP53), corresponding to earlier and later events in CLL evolution (Landau et al., Cell 152, 714-726, February 14, 2013). Leukemia cells were sampled from 18 patients at two time points and ten of twelve CLL eases treated with chemotherapy (but only one of six without treatment) underwent clonal evolution, predominantly involving subclones with driver mutations (e.g., SF3B1 and TP53) that expanded over time. The presence of a subclonal driver mutation was an independent risk factor for rapid disease progression. The study uncovered patterns of clonal evolution in CLL, providing insights into its stepwise transformation, and links the presence of subclones with adverse clinical outcomes(Landau et a!,, Cell 152, 714-726, February 14, 2013).

[00126] To study clonal evolution in CLL, integrative analysis of sCNAs and sSNVs was performed using an algorithm ABSOLUTE (Carter et al., 2012, Nat. Biotechnol. 30, 413-421), which jointly estimated the purity of the sample (fraction of cancer nuclei) and the average ploidy of the cancer ceils. As shown in Figure 2 of Landau et al., Cell 152, 714-726, February 14, 2013, CLL driver events were identified by mutation significance analysis using whole exome sequencing (Gnirke et al., 2009, Nat, Biotechnol. 27, 182-1 89) and SNP array data collected from matched germline and tumor DNA. For the 149 samples that had matched WES and copy number data, ABSOLUTE was applied to estimate the cancer cell fraction (CCF). Mutations were classified as subclonal or clonal, based on the probability that their CCF is greater than 0.95 (clonal). In a representative example of the transformations generated by ABSOLUTE, first, probability density distributions of allelic fractions for each mutation were plotted . Second, these data are converted to CCF, incorporating purity and local copy number information. The probability of the event being clonal (i.e., affecting >0.95 of cells) was represented by a color spectrum.

00127] In the method of Landau et al., Cell 152, 714-726, February 14, 2013, DNA was extracted from blood- or marrow-derived lymphocytes (tumor) and autologous epithelial cells (saliva), fibroblasts, or granulocytes (normal). libraries for WES were constructed and sequenced on either an Illumina HiSeq 2000 or GA-IIX using 76 bp paired-end reads (Berger et al., 201 1, Nature 470, 214-220; Chapman et al, 201 1 , Nature 471, 467-472). Output from Illumina software was processed by the Pi card data processing pipeline to yi eld BAM fil es containing well-calibrated, aligned reads (Chapman et al., 2011, Nature 470, 214-220; DePristo et al, 2011, Nat. Genet. 43, 491-498). sS^'NVs and indels were identified using MuTect (V I 19, [Cibulskis et al, 2013, Nat, Biotech. Published online February 10, 2013. http://dx.doi.org/i0.1038/nbt.2514.]) and indelocator (V61 , [Wang et al, 2011, N, Engl. J. Med. 365, 2497-2506]), respectively. Recurrent sSNV and indels in 160 CLLs were identified using MutSig2.0 (Lohr et al., 2012, Proc. Natl. Acad. Sci. USA 109, 3879-3884). For 111 of 149 matched CLL-normal DNA samples, copy number profiles were obtained using the Affymetrix Genome-wide Human SNP Array 6.0, with allele-specific analysis (HAPSEG [Carter et al., 2011, Nat. Biotechnol. 30, 413-421]). Recurrent sCNAs were identified using the GISTIC2.0 algorithm (Mermel et al., 2011 , Genome Biol. 12, R41 ), after excluding germ!ine copy number variants. For CLL samples with no available SNP arrays (38 of 149 CLLs), sCNAs were estimated directly from the WES data based on the ratio of CLL sample read -depth to the average read-depth observed in normal samples for that region. ABSOLUTE was applied to estimate sample purity, ploidy, and absolute somatic copy numbers. These were used to infer the CCFs of point mutations from the WES data. Following the framework previous!)' described (Carter et al, 2012, Nat. Biotechnol. 30, 413-421), the posterior probability distribution was computed over CCF c as follows. Consider a somatic mutation observed in a of N sequencing reads on a locus of absolute somatic copy number q in a sample of purity a. The expected allele - fraction f of a mutation present in one copy in a fraction c of cancer cells is calculated by . Then, , assuming a uniform prior on c. The distribution over CCF was then obtained by calculating these values over a regular grid of 100 c values and normalizing by dividing them by their sum, which is the constant of proportionality in the above equation. Mutations were thereafter classified as clonal based on the posterior probability that the CCF exceeded 0.95 and subelonal otherwise. Validation of allelic fraction was performed by using deep sequencing with indexed libraries recovered on a Fluidigm chip. Resulting normalized libraries were loaded on a MiSeq instrument (Jllumina) and sequenced using paired-end 150 bp sequencing reads to an average coverage depth of 4,200x. Associations between mutation rates and clmical features were assessed by the Wilcoxon rank-sum test. Fisher exact test, or the Kruskal-Wallis test, as appropriate. Time to event data were estimated by the method of Kaplan and Meier, and differences between groups were assessed using the logrank test. Unadjusted and adjusted Cox modeling was performed to assess the impact of the presence of a subelonal driver on clinical outcome measures alone and in the presence of clinical features known to impact outcome. A chisquare test with 1 degree of freedom and the -2 Log-likelihood statistic were used to test the prognostic independence of subelonal status in Cox modeling. [00128] As referred to herein, MuTect is a method developed for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes as detection of somatic point substitutions is a key step in characterizing the cancer genome. However, existing methods typically miss low-allelic-fraction mutations that occur in only a subset of the sequenced cells owing to either tumor heterogeneity or contamination by normal cells. MuTect is a method that applies a Bayesian classifier to detect somatic mutations with very low allele fractions, requiring only a few supporting reads, followed by carefully tuned filters that ensure high specificity (Cibulskis et ah, 2013, Nature Biotechnology, 31 , 3, 213-219). Cibulskis et al., 2013, Nature Biotechnology, 31, 3, 213-219 also describe benchmarking approaches that use real, rather than simulated, sequencing data to evaluate the sensitivity and specificity as a function of sequencing depth, base quality and allelic fraction. Compared with other methods, MuTect has higher sensitivity with similar specificity, especially for mutations with allelic fractions as low as 0.1 and below, making MuTect particularly useful for studying cancer subclones and their evolution in standard exome and genome sequencing data.

[00129] The virtual-tumor approach begins with deep-coverage data from a high-coverage, whole-genome sample (NA12878) sequenced on lilumina HiSeq instruments: two libraries (1000 Genomes Project Consortium. Nature 467, 1061-1073 (2010)), 'Solexa-18483' and 'Solexa- 18484', at 30* each and one library (Gnerre, 8. et al. Proc. Natl. Acad. Sci. USA 108, 1513- 1518 (2011)), 'Solexa-23661 ', at 3Qx, First, the sequencing data was randomly divided into several partitions. Six partitions were created from each of the three libraries ( 18 partitions total), therefore creating data partitions with ~5 ^x coverage each. This was accomplished by sorting the BA 39 by name using SortSam from the Pieard (http://picard.sourceforge.net/) tools to effectively give the reads random ordering. Each read was randomly allocated to one of the partitions and wrote it to a partition-specific BAM file.

[00130] To measure specificity, certain partitions may be designated as the 'tumor' and others as the 'normal', and processed through MuTect (or any other method). Somatic mutations identified in this process are false positives as they are either germ-line events that are undercalied in the normal or erroneous variants resulting from sequencing noise overcalled in the partitions designated as tumor. Reads from libraries Solexa-18483 and Solexa-23661 were drawn for the tumor sample and from the library Solexa- 18484 for the normal sample. [00131] To measure sensitivity, additional sequencing data was turned to on a second individual. In this case NA12891 was chosen, which was also sequenced to 60* as part of the 1000 Genomes Project, Using the published high-confidence single-nucleotide polymorphism (S P) genotypes for those samples from the 1000 Genomes Project, a set of sites was identified that are heterozygous in NA12891 and homozygous for the reference in NA12878.

[00132] A second utility, SomaticSpike, which is part of the MuTect software package, was used to perform a mixing experiment in silico. At each of the selected sites, this utility attempts to replace a number of reads determined by a binomial distribution using a specified allelic fraction in the NA12878 data with reads from the NA 12891 data, therefore simulating a somatic mutation of known location, type and expected allele fraction. If there are not enough reads in NA12891 to replace the desired reads in ΝΛ 12878. the site is skipped,

[0Θ133] The output of this process is a virtual tumor BAM with the in silico variants and a set of locations of those variants. Sensitivity is then estimated by attempting to detect mutations at these sites.

[00134] For each site the reference allele was denoted as r E { A,C,G,T} and denoted by bi and ei the called base of read i (i = 1 . . ,d) that covers the site and the probability of error of that base call (each base has an associated Phred-like quality score qi where *¾ ^{= 1}° To call a variant in the tumor the data is explained using two models: (i) model M0 in which there is no variant at the site and all nonreference bases are explained by sequencing noise, and (ii) model f in which a variant allele m truly exists at the site with an allele fraction f and, as in M0, reads are also subject to sequencing noise. Note that M0 is equivalent to with f = 0,

[00135] The likelihood of the model ^A is given by s"⁵

assuming the sequencing errors are independent across reads. If all substitution errors are equally likely, that is, occur with probability , the following is obtained:

[00136] Variant detection is performed by comparing the likelihood of both models and if their ratio, that is, the LOD score, exceeds a decision threshold (loglO δΤ) m is declared as a candidate variant at the site. The following is calculated

and set δΤ to 2 to ensure that at least two times confidence that the site is variant as compared to noise. LODT can also be rewritten as:

[00137] To determine P(m,f), first assume that P(m) and P(f) are statistically independent and that P(f) is uniformly distributed (that is, P(f) ^::: 1) and P(m) is one-third of the expected mutation frequency for the studied tumor type (representing equal prior for all substitutions), in practice, a typical mutation frequency of 3 ^x 10-6 was used, which yields ΘΤ = 6.3.

[00138] The maximum LODT was found across all three values of m and to set the unknown allelic fraction parameter f, a maximum likelihood estimation could be used, that is, find f that maximizes LODT. However, for computational efficiency, an estimate was

.,_r _ asiisberoi fisaiasi reads

' naittherof total reads

[00139] A common source of false positive mutation calls is contamination of the tumor DNA with DNA. from other individuals. Germ-line SNPs in the contaminating DNA appear as somatic mutations. It was previously demonstrated that such contamination can yield many false positives and a tool was developed , ContEst (Cibulskis, . et al. Bioinformatics 2.7, 2601-2602 (2011)), to estimate the contamination level, f_cont, hi sequencing data. Low-level contamination of DNA is a common phenomenon, and even 2% contamination can give rise to 166 false positive calls per megabase and 10 false positive calls per megabase when excluding known SNP sitesfCibulskis, . et al. Bioinformatics 27, 2601 -2602 (201 1)). To protect against this type of false positives and enable analysis of contaminated samples, the reference model was replaced with a variant model, ^Λί This guarantees that variants are called only when they are highly unlikely to be explained by contamination.

[00140] To reduce false positives and miscalled germ-line events, a panel of nonnal samples was used as a filter. To create this filter, MuTect was am on a set of normal samples as if they were tumor samples without a matched nonnal sample in STD mode. From these data, a VCF file is created for the sites that were identified as variant by MuTect in more than one normal sample. This VCF is then supplied to the caller, which rejects these sites. However, if the site was present in the supplied VCF of known mutations it is retained because these sites could represent known recurrent somatic mutations that have been detected in the panel of normal samples when the normal samples are from adjacent tissue or have some contamination tumor D^'NA. The more normal samples are used to construct this panel the higher the power will be to detect and remove rare artifacts. Therefore, typically all the normal samples readily available were used. The results were obtained by using a panel of whole-genome sequencing data from blood normal samples of 125 patients with solid tumor cancer. The samples used as part of the virtual-tumor approach were not included in this panel.

[00141] To perform this classification, a similar classifier was used to the one described above. In this case, f in ^Μϊ was conservatively set to 0.5 for a germ-line heterozygous variant.

can be rewritten

. Note that here the terms are inverted because there should be confidence that alteration was not present. For 6N, a threshold of 10 was set, which is higher than the threshold for δΤ because variant classification misclassified as germ-line events will quickly appear to be significant in downstream somatic analysis owing to their elevated population frequency at recurrent sites as compared to real somatic events.

[00142] To calculate P(geroi line) two cases were distinguished: (i) sites which are known to be variant in the population and (ii) all other sites. The public dbSNP database (Sherry, S.T. et al. Nucleic Acids Res. 29, 308-311 (2001)) was used to make this distinction.

[00143] There are -30 ^x 10e6 sites known to be variant in the human population according to dbSNP release 134, which is -1 ,000 variants/Mb. A given individual typically has ~3 ^x 10e6 variants in their genome, 95% of which are in dbSNP sites (Sherry, S.T. et al. Nucleic Acids Res. 29, 308-311 (2001) and 1000 Genomes Project Consortium. Nature 467, 1061 -1073 (2010)). Therefore ~50 variants/Mb are expected not at dbSNP sites, that is, P(germ linejnon-dbSNP site) = 5 x 10e-5 and therefore 0N|non-dbSNP site = 2.2 is used. At dbSNP sites, however, 95% of the ~3 x 10e6 variants are expected to occur in the 30 x 10e6 sites in the dbSNP database, yielding P(germ line!dbSNP site) = 0.095, hence GN!dbSNP site ==^: 5.5. [00144] To calculate the sensitivity to detect a mutation with allelic fraction f using n reads having a Phred-like quality score q (and hence a base error, e, of ^i>:i), k, the minimum number of reads with the alternate allele that will trigger a variant call is calculated using k = argsnin ίΟύγ{^χ ≥θγ

[00145] The sensitivity is then the probability of observing k or more reads given the allelic fraction and depth. The marginal distribution of the number of reads with the alternate allele, either originating from the alternate base or a misread reference base, follows a binomial distribution with a frequency that reflects the true underlying allelic fraction f and the probability of error e (note that here the worst case is taken in which all misread bases convert to the same alternate allele . Therefore the probability of having observed k or more reads can be calculated

[00146] As referred to herein, ContEst is a tool (and method) for estimating the amount of cross-sample contamination in next generation sequencing data. Using a Bayesian framework, contamination levels are estimated from array based genotypes and sequencing reads. This is further described in Cibulskis et al., ContEst: Estimating cross-contamination of human samples in next generation sequencing data, Bioinfomiatics (2011) doi: 10.1093/bioinformatics/btr446 First published online: July 29, 2011.

[00147] As referred to herein, dRanger is a tool to identify somatic rearrangements as clusters of aberrant paired-end sequencing reads in a tumor sample where the normal sample has read- pairs consistent with the reference. Candidate rearrangement breakpoints from dRanger are passed into Breakpointer, which applies a modified Smith- Waterman algorithm to ail reads in the region to identify split-read support for the rearrangement.

[0Θ148] As referred to herein. Firehose is an analysis infrastructure developed to coordinate the flow of terabyte-scale datasets through dozens of quantitative algorithms. Implemented primarily as a Java web application, the chief aims of Firehose are reproducibility, automation, and high throughput. To achieve the first of these goals Firehose version-tracks samples, algorithms, and the logic which binds them together, storing this and related execution information in a persistent RDBMS for provenance; this makes it easy for users to identify, over arbitrarily large time spans, what has been run, what can be run, what needs to be run again if data or algorithms change, or what cannot be ran due to unsatisfied dependencies.

[0Θ149] Automation and throughput are facilitated in several ways: First, while Firehose is most often used interactively from a browser, it also offers an extensive API for programmatic control of routine tasks and scalability to multiple workspaces and datasets. Next, by encapsulating data and algorithm parameters within abstract annotations, instead of only literal values or explicit file system references, Firehose is able to execute analyses in data-blind manner across a wide variety of inputs, without modification or onerous bookkeeping for end users. This has proven to be a powerful metaphor for interacting with TCGA data, for example, because once an algorithm is in Firehose it can run on either a single tumor type or all of them with equal ease. Third, encapsulating jobs within an abstract execution engine (presently GenePattern, but support for others is under development) enables them to be transparently dispatched to a single machine or across many compute nodes, again without algorithm modification or extensive user tuning; in-depth knowledge of the underlying operating system or PC task scheduler is not required, as entire analysis workflows for all samples of interest can be executed at the click of a button or via one API call. Finally, provenance stored for reproducibility also increases throughput by allowing new job requests that match previous requests to be completely avoided; in these cases Firehose simply returns the prior results.

[0Θ150] Although still evolving, Firehose was developed at The Broad Institute and has become a valuable piece of computing frastructure used daily by dozens in the Cancer Genome Analysis group, to perform all TCGA GDAC and GSC analyses, managing hundreds of thousands of jobs on tens of thousands of samples, spread over hundreds of compute nodes and a 400+ TB file system.

[00151] As referred to herein, Indelocator is a software tool for calling short indels in next generation sequencing data. Indelocator is mainly the engine for collecting various read count and alignment quality-related statistics around putative indel events. It does not perform realignment or split-read alignment, but relies on the alignments already recorded in the input bam file(s). It is thus very important to use well-aligned input bam files, as misaligned reads will not be corrected and will not be counted towards their correct allele. Running local realignment around indels algorithm from GAT is highly recommended prior to using Indelocator. [00152] In its default mode, Indelocator uses two input bam files (or two sets of input files), for normal and tumor samples. Events present in tumor sample above the specified thresholds and having sufficient coverage in normal sample (another input parameter) are recorded in the output alongside with various alignment metrics, and are also annotated as (putative!)') germline or somatic depending on the presence of the alternative allele in normal sample (see GATK documentation for more detail). Indelocator also supports single-sample mode, in which it tallies same alignment metrics around each putative indel event in a (single) sample. Output of Indelocator is a high-sensitivity list of putative indel events containing large numbers of false positives. The statistics reported for each event have to be used to custom-filter the list in order to lower false positive rate.

[00153] As referred to herein, Oncotator is a tool for annotating human genomic point mutations and indeis with data relevant to cancer researchers. Annotations are aggregated from the following resources:

[00154] Genomic Annotations

- Gene, transcript, and functional consequence annotations using UCSC KnownGenes hgl9 and mirBase reference sets.

- Common SNP annotations from dbSNP (includes data from 1000 Genomes project pilot 1, 2, and 3 studies).

[00155] Protein Annotations

- Site-specific protein annotations from UniProt,

- Druggabie target data from DrugBank.

- Functional impact predictions from PolyPhen-2 is to be incorporated.

Cancer Annotations

- Observed cancer mutation frequency annotations from COSMIC.

- Cancer gene and mutation annotations from the Cancer Gene Census.

- Significant amplification/deletion region annotations from Tumorscape and the TCGA Copy Number Portal.

- Overlapping Oncomap mutations from the Cancer Cell Line Encyclopedia,

- Significantly mutated gene annotations aggregated from published MutSig analyses.

- Cancer gene annotations from the Familial Cancer Database. - Human DNA Repair Gene annotations from Wood et ai. (Human DNA Repair Genes, Science 291, 1284 (2001); Mutation Res. 577, 275 (2005)).

[0Θ156] As referred to herein, RefSeq is the NCBI Reference Sequence Database which is a comprehensive, integrated, non -redundant, well-annotated set of reference sequences including genomic, transcript, and protein,

[00157] As referred to herein, The Cancer Gene Census (CGC) is an ongoing effort to catalogue those genes for which mutations have been causally implicated in cancer. The original census and analysis was described in Futreal et al. "A census of human cancer genes" Nature Reviews Cancer 4, 177- 183 (March 2004). It is a manually curated list of at least 375 genes mutated in several types of cancer, e.g., Leukemia (230), Epithelial cancers (1 15), Mesenchimal cancers (76), and Other cancer types (41).

[0Θ158] As referred to herein, COSMIC is designed to store and display somatic mutation information and related details and contains information relating to human cancers. COSM IC is an online database of somatically acquired mutations found in human cancer. COSMIC, an acronym of Catalogue Of Somatic Mutations In Cancer, curates data from papers in the scientific literature and large scale experimental screens from the Cancer Genome Project at the Sanger Institute. Some key features of COSMIC are: 1) Contains information on publications, samples and mutations. Includes samples which have been found to be negative for mutations during screening therefore enabling frequency data to be calculated for mutations in different genes in different cancer types. 2) Samples entered include benign neoplasms and other benign proliferations, in situ and invasive tumors, recurrences, metastases and cancer cell lines, 3) The mutation data and associated information is extracted from the primar iiterature and entered into the COSMIC database. In order to provide a consistent view of the data a histology and tissue ontology has been created and all mutations are mapped to a single version of each gene. The data can be queried by tissue, histology or gene and displayed as a graph, as a table or exported in various formats.

[00159] As referred to herein, Gene Pattern is a powerful genomic analysis platform that provides access to more than 240 tools for gene expression analysis, proteomics, SNP analysis, flow cytometry, RNA-seq analysis, and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research, (further description is available at the website broadiastitute.org cancer/sofhvare/genepattern/)

[00160] As referred to herein, Picard or Picard pipelines are production pipelines that feed computational pipelines of groups at the Broad Institute which include but are not limited to Cancer mutation and rearrangement detection, Medical Genetics variant calling and Automated microbial assembly.

[00161] Clinical relevance refers to a principle, fact, or study that is directly applicable to patient care. It relates to the bedside of a patient, the course of his or her disease, or the observation and treatment of patients directly. The term encompasses clinical significance. In medicine and psychology, clinical significance refers to either of two related but slightly dissimilar concepts whereby certain findings or differences, even if measurable or statistically confirmed, either may or may not have additional significance, either by (I) being of a magnitude that conveys practical relevance (a usage that conflates practical and clinical significance interchangeably), or (2) more technically and restrictively, addresses whether an intervention or treatment may or may not fully correct the finding. Biological relevance refers to a principle, fact or study that relates to affecting life or living organisms as relates to systems and pathways at the molecular, cellular or systems levels that occur in an organism. The term encompasses biological significance. What is biologically or clinically significant is measured in terms of a biological outcome (e.g., difference in measures such as morbidity or mortality, difference in weight gain). Many studies with statistically insignificant findings are not of sufficient size to detect the minimum clinical or biological significant difference. Conversely, with a large enough sample size any study will obtain statistical significance for differences that are too small to have any biological or clinical significance.

[00162] The practice of analysis related to the present invention employs, unless otherwise indicated, conventional techniques of immunology, biochemistry, chemistry, molecular biology, microbiology, cell biology, genomics and recombinant DNA, which are within the skill of the art. See Sambrook, Fritsch and Maniaris, MOLECULAR CLONING: A LABORATORY MANUAL, 2nd edition (1989); CURRENT PROTOCOLS IN MOLECULAR BIOLOGY (F. M. Ausubel, et al. eds., (1987)); the series METHODS IN ENZYMOLOGY (Academic Press, Inc.): PGR 2: A PRACTICAL APPROACH (M.J. MacPherson, B.D. Hames and G.R. Taylor eds. (1995)), Harlow and Lane, eds. (1988) ANTIBODIES, A LABORATORY MANUAL, and ANIMAL CELL CULTURE (R.I. Freshney, ed. (1987)). A few of these techniques are further described in brief below.

[00163] The sequences referred to herein may also have deletions, insertions or substitutions of amino acid residues which produce a silent change and result in a functionally equivalent subuStance. Deliberate amino acid substitutions may be made on the basis of similarity in amino acid properties (such as polarity, charge, solubility, hydrophobicity, hydrophiiicity, and/or the amphipathic nature of the residues) and it is therefore useful to group amino acids together in functional groups. Amino acids may be grouped together based on the properties of their side chains alone. However, it is more useful to include mutation data as well. The sets of amino acids thus derived are likely to be conserved for structural reasons. These sets may be described in the form of a Venn diagram (Livingstone CD. and Barton G.J. (1993) "Protein sequence alignments: a strategy for the hierarchical analysis of residue conservation" Comput. Appl. Biosci. 9: 745-756) (Taylor W.R, (1986) "The classification of amino acid conservation" J, Theor. Biol. 119; 205-218). Conservative substitutions may be made, for example according to the table below which describes a generally accepted Venn diagram grouping of amino acids.

[0Θ164] Sequences (both polynucleotide or polypeptide) mentioned herein may comprise homologous substitution (substitution and replacement are both used herein to mean the interchange of an existing amino acid residue or nucleotide, with an alternative residue or nucleotide) that may occur i.e., like -for- like substitution in the case of amino acids such as basic for basic, acidic for acidic, polar for polar, etc. Non-homologous substitution may also occur i.e., from one class of residue to another or alternatively involving the inclusion of unnatural amino acids such as ornithine (hereinafter referred to as Z), diaminobutyric acid ornithine (hereinafter referred to as B), norleucine ornithine (hereinafter referred to as O), pyriylalanine, thieiiylaianiiie, naphthylalanine and phenyiglycine.

[00165] Variant amino acid sequences may include suitable spacer groups that may be inserted between any two amino acid residues of the sequence including alkyl groups such as methyl, ethyl or propyl groups in addition to amino acid spacers such as glycine or β-alanine residues. A further form of variation, which involves the presence of one or more amino acid residues in peptoid form, may be well understood by those skilled in the art. For the avoidance of doubt, "the peptoid form" is used to refer to variant amino acid residues wherein the a-carbon substituent group is on the residue's nitrogen atom rather than the a-carbon. Processes for preparing peptides in the peptoid form are known in the art, for example Simon RJ et al, P AS (1992) 89(20), 9367-9371 and Horwell DC, Trends Biotechnol. (1995) 13(4), 132-134.

[0Θ166] An altered expression of one or more genome sequences associated with a signaling biochemical pathway can be determined by assaying for a difference in the mRNA levels of the corresponding genes between the test model cell and a control ceil, when they are contacted with a candidate agent. Alternatively, the differential expression of the sequences associated with a signaling biochemical pathway is determined by detecting a difference in the level of the encoded polypeptide or gene product. To assay for an agent-induced alteration in the level of mRNA transcripts or corresponding polynucleotides, nucleic acid contained in a sample is first extracted according to standard methods in the art. For instance, mRNA can be isolated using various lytic enzymes or chemical solutions according to the procedures set forth in Sambrook et al. (1989), or extracted by nucleic-acid-binding resins following the ac companying instructions provided by the manufacturers. The mRNA contained in the extracted nucleic acid sample is then detected by amplification procedures or conventional hybridization assays (e.g., Northern blot analysis) according to methods wide!)' known in the art or based on the methods exemplified herein.

[00167] As used herein the term "amplification" means any method employing a primer and a polymerase capable of replicating a target sequence with reasonable fidelity. Amplification may be carried out by natural or recombinant DNA polymerases such as TaqGold™, T7 DNA polymerase, Klenow fragment of E.coli DNA polymerase, and reverse transcriptase, A preferred amplification method is PCR. In particular, the isolated RNA can be subjected to a reverse transcription assay that is coupled with a quantitative polymerase chain reaction (RT-PCR) in order to quantify the expression level of a sequence associated with a signaling biochemical pathway.

[00168] Detection of the gene expression level can be conducted in real time in an amplification assay. In one aspect, the amplified products can be directly visualized with fluorescent DNA-binding agents including but not limited to DNA intercalators and DNA groove binders. Because the amount of the intercalators incorporated into the double-stranded DNA molecules is typically proportional to the amount of the amplified DNA. products, one can conveniently determine the amount of the amplified products by quantifying the fluorescence of the intercalated dye using conventional optical systems in the art, DNA-binding dye suitable for this application include SYBR green, SYBR blue, DAPI, propidium iodine, Hoeste, SYBR gold, ethidium bromide, acridities, proflavine, acridiiie orange, acriflavine, fluorcoumamn, eilipticine, daunomycin, chloroquine, distamycin D, ehrornornycin, homidium, mithramycin, ruthenium polypyridyis, anthramycin, and the like.

[00169] In another aspect, other fluorescent labels such as sequence specific probes can be employed in the amplification reaction to facilitate the detection and quantification of the amplified products. Probe-based quantitative amplification relies on the sequence-specific detection of a desired amplified product. It utilizes fluorescent, target-specific probes (e.g., TaqMan® probes) resulting in increased specificity and sensitivity. Methods for performing probe-based quantitative amplification are well established in the art and are taught in U.S. Patent No. 5,210,015.

[00170] In yet another aspect, conventional hybridization assays using hybridization probes that share sequence homology with sequences associated with a signaling biochemical pathway can be performed. Typically, probes are allowed to form stable complexes with the sequences associated with a signalmg biochemical pathway contained within the biological sample derived from the test subject in a hybridization reaction. It will be appreciated by one of skill in the art that where antisense is used as the probe nucleic acid, the target polynucleotides provided in the sample are chosen to be complementary to sequences of the antisense nucleic acids. Conversely, where the nucleotide probe is a sense nucleic acid, the target polynucleotide is selected to be complementary to sequences of the sense nucleic acid.

[00171] Hybridization can be performed under conditions of various stringency. Suitable hybridization conditions for the practice of the present invention are such that the recognition mteraction between the probe and sequences associated with a signaling biochemical pathway is both sufficiently specific and sufficiently stable. Conditions that increase the stringency of a hybridization reaction are widely known and published in the art. See, for example, (Sambrook, et al., (1989); Nonradioactive In Situ Hybridization Application Manual, Boehringer Mannheim, second edition). The hybridization assay can be formed using probes immobilized on any solid support, including but are not limited to nitrocellulose, glass, silicon, and a variety of gene arrays. A preferred hybridization assay is conducted on high-density gene chips as described in U.S. Patent No. 5,445,934.

[00172] For a convenient detection of the probe-target complexes formed during the hybridization assay, the nucleotide probes are conjugated to a detectable label. Detectable labels suitable for use in the present invention include any composition detectable by photochemical, biochemical, spectroscopic, immunochemical, electrical, optical or chemical means. A wide variety of appropriate detectable labels are known in the art, which include fluorescent or chemiluminescent labels, radioactive isotope labels, enzymatic or other ligands. In preferred embodiments, one will likely desire to employ a fluorescent iabel or an enzyme tag, such as digoxigenin, β-galactosidase, urease, alkaline phosphatase or peroxidase, avidin/biotin complex.

[00173] The detection methods used to detect or quantify the hybridization intensity will typically depend upon the label selected above. For example, radiolabels may be detected using photographic film or a phosphoimager. Fluorescent markers may be defected and quantified using a photodetector to detect emitted light. Enzymatic labels are typically detected by providing the enzyme with a substrate and measuring the reaction product produced by the action of the enzyme on the substrate; and finally colorimetric labels are detected by simply visualizing the colored label.

[0Θ174] An agent-induced change in expression of sequences associated with a signaling biochemical pathway can also be determined by examining the corresponding gene products. Determining the protein level typically involves a) contacting the protein contained in a biological sample with an agent that specifically bind to a protein associated with a signaling biochemical pathway; and (b) identifying any agent:protein complex so formed. In one aspect of this embodiment, the agent that specifically binds a protein associated with a signaling biochemical pathway is an antibody, preferably a monoclonal antibody. The reaction is performed by contacting the agent with a sample of the proteins associated with a signaling biochemical pathway derived from the test samples under conditions that will allow a complex to form between the agent and the proteins associated with a signaling biochemical pathway. The formation of the complex can be detected directly or indirectly according to standard procedures in the art. In the direct detection method, the agents are supplied with a detectable label and unreacted agents may be removed from the complex; the amount of remaining label thereby indicating the amount of complex formed. For such method, it is preferable to select labels that remain attached to the agents even during stringent washing conditions. It is preferable that the label does not interfere with the binding reaction. In the alternative, an indirect detection procedure may use an agent that contains a label introduced either chemically or enzymatically. A desirable label generally does not interfere with binding or the stability of the resulting agent polypeptide complex. However, the label is typically designed to be accessible to an antibody for an effective binding and hence generating a detectable signal. A wide variety of labels suitable for detecting protein levels are known in the art. Non-limiting examples include radioisotopes, enzymes, colloidal metals, fluorescent compounds, biolummescent compounds, and chemiiumiiiescent compounds.

[00175] The amount of agent:polypeptide complexes formed during the binding reaction can be quantified by standard quantitative assays. As illustrated above, the formation of agen polypeptide complex can be measured directly by the amount of label remained at the site of binding. In an alternative, the protein associated with a signaling biochemical pathway is tested for its ability to compete with a labeled analog for binding sites on the specific agent. In this competitive assay, the amount of label captured is inversely proportional to the amount of protein sequences associated with a signaling biochemical pathway present in a test sample.

[00176] A number of techniques for protein analysis based on the general principles outlined above are available in the art. They include but are not limited to radioimmunoassays, ELISA (enzyme linked immunoradiometric assays), "sandwich" immunoassays, immunoradiometric assays, in situ immunoassays (using e.g., colloidal gold, enzyme or radioisotope labels), western blot analysis, immunoprecipitation assays, immunofluorescent assays, and SDS-PAGE. [00177] Antibodies that specifically recognize or bind to proteins associated with a signaling biochemical pathway are preferable for conducting the aforementioned protein analyses. Where desired, antibodies that recognize a specific type of post-translational modifications (e.g., signaling biochemical pathway inducible modifications) can be used. Post-translational modifications include but are not limited to glycosylation, iipidation, acetylation, and phosphorylation . These antibodies may be purchased from commercial vendors. For example, anti-phosphotyrosine antibodies that specifically recognize tyrosine-phosphorylated proteins are available from a number of vendors including Invitrogen and Perkin Elmer. Anti- phosphotyrosine antibodies are particularly useful in detecting proteins that are differentially phosphorylated on their tyrosine residues in response to an ER stress. Such proteins include but are not limited to eukaryotic translation initiation factor 2 alpha (elF-2a). Alternatively, these antibodies can be generated using conventional polyclonal or monoclonal antibody technologies by immunizing a host animal or an antibody-producing cell with a target protein that exhibits the desired post-translational modification.

[00178] It may be desirable to discern the expression pattern of an protein associated with a signaling biochemical pathway in different bodily tissue, in different cell types, and/or in different subcellular structures. These studies can be performed with the use of tissue-specific, cell-specific or subcellular structure specific antibodies capable of binding to protein markers that are preferentially expressed in certain tissues, cell types, or subcellular structures.

[00179] An altered expression of a gene associated with a signaling biochemical pathway can also be determined by examining a change in activity of the gene product relative to a control cell. The assay for an agent-induced change in the activity of a protein associated with a signaling biochemical pathway will dependent on the biological activity and/or the signal transduction pathway that is under investigation. For example, where the protein is a kinase, a change in its ability to phosphorylate the downstream substrate(s) can be determined by a variety of assays known in the art. Representative assays include but are not limited to immunob lotting and immunoprecipiiation with antibodies such as anti-phosphotyrosine antibodies that recognize phosphorylated proteins. In addition, kinase activity can be detected by high throughput chemiluminescent assays such as AlphaScreen™ (available from Perkin Elmer) and eTag™ assay (Chan-Hui, et al. (2003) Clinical Immunology I I I : 162-174). [00180] Where the protein associated with a signaling biochemical pathway is part of a signaling cascade leading to a fluctuation of intracellular pH condition, pH sensitive molecules such as fluorescent pH dyes can be used as the reporter molecules. In another example where the protein associated with a signaling biochemical pathway is an ion channel fluctuations in membrane potential and/or intracellular ion concentration can be monitored. A number of commercial kits and high-throughput devices are particularly suited for a rapid and robust screening for modulators of ion channels. Representative instruments include FLIPR ^rM (Molecular Devices, Inc.) and VIPR (Aurora Biosciences). These instruments are capable of detecting reactions in over 1000 sample wells of a microplate simultaneously, and providing real-time measurement and functional data within a second or even a millisecond.

[00181 J The invention comprehends generating information that may be useful in creating an animal or cell that may be used as a disease model. As used herein, "disease" refers to a disease, disorder, or indication in a subject. For example, methods of the invention may relate to creating an animal or ceil that comprises a modification in one or more nucleic acid sequences associated with a disease, or an animal or cell in which the expression of one or more nucleic acid sequences associated with a disease are altered. Such a nucleic acid sequence may encode a disease associated protein sequence or may be a disease associated control sequence.

[00182] In some methods, the disease model can be used to study the effects of mutations on the animal, e.g., human being or cell and development and/or progression of the disease using measures commonly used in the study of the disease. Alternatively, such a disease model is useful for studying the effect of a pharmaceutically active compound on the disease.

[00183] In some methods, the disease model can be used to assess the efficacy of a potential gene therapy strategy. That is, a disease-associated gene or polynucleotide can be modified such that the disease development and/or progression is inhibited or reduced. In particular, the method comprises modifying a disease-associated gene or polynucleotide such that an altered protein is produced and, as a result, the animal or cell has an altered response. Accordingly, in some methods, a genetically modified animal may be compared with an animal predisposed to development of the disease such that the effect of the gene therapy event may be assessed.

[00184] The invention comprehends generating information that may be useful in developing a biologically active agent that modulates a cell signaling event associated with a disease gene; and hence, other target genes or proteins encoded therefrom may also be identified that are subject to the modulation.

[0Θ185] The invention comprehends developing a cell model or animal model that can be constructed based on the information generated by the methods of the invention for screening a cellular function change. Such a model may be used to study the effects of a genome sequence identified in methods of the invention on a cellular function of interest. For example, a cellular function model may be used to study the effect of a modified genome sequence on intracellular signaling or extracellular signaling. Alternatively, a cellular function model may be used to study the effects of a modified genome sequence on sensory perception. In some such models, one or more genome sequences associated with a signaling biochemical pathway in the model are modified.

[0Θ186] A "disease-associated" gene or polynucleotide refers to any gene or polynucleotide which is yielding transcription or translation products at an abnormal level or in an abnormal form in cells derived from a disease-affected tissues compared with tissues or cells of a non disease control. It may be a gene that becomes expressed at an abnormally high level; it may be a gene that becomes expressed at an abnormally low level, where the altered expression correlates with the occurrence and/or progression of the disease. A disease-associated gene also refers to a gene possessing mutation(s) or genetic variation that is directly responsible or is in linkage disequilibrium with a gene(s) that is responsible for the etiology of a disease. The transcribed or translated products may be known or unknown, and may be at a normal or abnormal level.

[00187] A key aspect of the invention relates to evaluation and ranking of genes. These genes and other genes or proteins involved in the same cellular pathways may be considered in selecting treatment options for cancer patients or patients having tumors.

[00188] Examples of tumors, cancers or proliferative disorders include, but are not limited to, a carcinoma, for example a carcinoma of the bladder, breast, colon (e.g., colorectal carcinomas such as colon adenocarcinoma and colon adenoma), kidney, epidermis, liver, lung, for example adenocarcinoma, small cell lung cancer and non-small cell lung carcinomas, esophagus, gall bladder, ovary, pancreas e.g., exocrine pancreatic carcinoma, stomach, cervix, thyroid, prostate, gastrointestinal system, e.g., gastrointestinal stromal tumors, or skin, for example squamous cell carcinoma; a hematopoieitic tumor of lymphoid lineage, for example leukemia, acute lymphocytic leukemia, chronic lymphocytic leukemia, B-cel lymphoma (such as diffuse large B cell lymphoma), T-cell lymphoma, Hodgkin's lymphoma, non-Hodgkin's lymphoma, hairy cell lymphoma, or Burkitt's lymphoma; a hematopoieitic tumor of myeloid lineage, including, but not limited to acute myeloid leukemia, chronic myeloid leukemias, myelogenous leukemias, and Imatinib sensitive and refractory chronic myelogenous leukemias, myelodysplastic syndrome, Bortezomib sensitive and refractory multiple myeloma, myeloproliferative disease or promyelocytic leukaemia; thyroid follicular cancer; a tumor of mesenchymal origin, for example fibrosarcoma or rhabdomyosarcoma; a tumour of the central or peripheral nervous system, for example astrocytoma, neuroblastoma, glioma (a High grade glioma) or schwannoma; melanoma (e.g., malignant or metastatic melanoma); seminoma; teratocarcinoma; osteosarcoma; keratoacanthoma; thyroid follicular cancer; or Kaposi's sarcoma. A further example of a tumour of mesenchymal origin is Ewing's sarcoma,

[00189] One sub-group of cancers includes a carcinoma, for example a carcinoma of the bladder, breast, colon (e.g., colorectal carcinomas such as colon adenocarcinoma and colon adenoma), kidney, epidermis, liver, lung, for example adenocarcinoma, small cell lung cancer and non-small cell lung carcinomas, gall bladder, ovary, pancreas e.g., exocrine pancreatic carcinoma, stomach, thyroid, prostate, gastrointestinal system, e.g., gastrointestinal stromal tumors, or skin, for example squamous cell carcinoma; a hematopoieitic tumour of lymphoid lineage, for example leukemia, acute lymphocytic leukemia, chronic hTOpliQcytic leukemia, B- cell lymphoma (such as diffuse large B cell lymphoma), T-cell lymphoma, Hodgkin's lymphoma, non-Hodgkin's lymphoma, hairy cell lymphoma, or Burkitt's lymphoma; a hematopoieitic tumor of myeloid lineage, including acute myeloid leukemia, chronic myeloid leukemias, myelogenous leukemias, and Imatinib sensitive and refractory chronic myelogenous leukemias, myelodysplastic syndrome, Bortezomib sensitive and refractory multiple myeloma, myeloproliferative disease or promyelocytic leukemia; thyroid follicular cancer; a tumor of mesenchymal origin, for example fibrosarcoma or rhabdomyosarcoma; a tumor of the central or peripheral nervous system, for example astrocytoma, glioma (a High grade glioma); melanoma (e.g., malignant or metastatic melanoma); osteosarcoma; or thyroid follicular cancer. A further example of a tumor of mesenchymal origin is Ewing's sarcoma.

[00190] One group of cancers consists of solid tumors selected from metastatic breast cancer which is HE 2 positive; adenocarcinoma of the prostate; metastatic melanoma; non-small cell carcinoma of the lung (NSCLC); small cell carcinoma of the lung (SCI.C); high grade gliomas; gastrointestinal stromal tumors (GIST); colorectal cancer; glioblastoma; melanoma; metastatic thyroid cancer; prostate cancer; and rectal cancer.

[00191] Within this group of cancers, a particular subgroup consists of colorectal cancer; glioblastoma; melanoma; metastatic thyroid cancer; prostate cancer; and rectal cancer.

[00192] One group of cancers includes human breast cancers (e.g., primary breast tumors, node-negative breast cancer, invasive duct adenocarcinomas of the breast, non-endometrioid breast cancers); and mantle cell lymphomas. In addition, other cancers are colorectal and endometrial cancers.

[00193] Another sub-set of cancers includes hematopoietic tumors of both lymphoid and myeloid lineage, for example acute lymphoblastic leukemia, chronic lymphocytic leukemia (Both T and B ceil), acute myeloid leukemia, chronic myeloid leukemia, mantle ceil lymphoma and B-cell lymphoma (such as diffuse large B cell lymphoma) and optionally further includes chronic myelogenous leukemia and multiple myeloma.

[00194] A sub-set of cancers consists of ErbB2 -positive breast, prostate, lung, and gastric cancer; chronic myeloid leukemia; androgen receptor dependent prostate cancer; Flt3 -dependent acute myeloid leukemia; melanoma associated with Braf mutation; multiple myeloma; velcade refractory multiple myeloma; and gastrointestinal stromal tumors (GIST). Overexpression of ErbB2 (HER-2) occurs in approximately 30% of breast cancers and is linked to poor prognosis and drug resistance (Tsugawa et. al, 1993. Oncology 1993; 50: 418).

[0Θ1 5] Of these, particularly cancers are multiple myelomas and velcade refractory tumor types as defined herein. The present invention may be used in the treatment of Velcade refractory tumour types including treatment of patients with multiple myeloma, mantle cell lymphoma, indolent non-Hodgkin's lymphoma, stage ΠΙΒ and IV Bronchioloalveolar carcinoma, advanced non-small cell lung cancer, breast, prostate and ovarian cancers and non-Hodgkin's lymphoma.

[001 6] Another sub-set of cancers consists of hormone refractory prostate cancer, metastatic melanoma, HER2 positive breast cancer, mutant EGFR positive non-small cell lung carcinoma and Gleevec resistant gastrointestinal stromal tumors.

[00197] Depending upon the cancer identified, follow up and palliative care is administered at that time. Certain disorders (such as acute lymphoblastic leukemia or acute myelogenous leukemia or acute nonlymphocytic leukemia) requires immediate admission and chemotherapy, while others are followed up with regular physical examination and blood tests

[0Θ1 8] Often, surgery is attempted to remove a tumor entirely. This is only feasible when there is some degree of certainty that the tumor can in fact be removed. When it is certain that parts remain, curative surgery is often impossible, e.g., when there are metastases elsewhere, or when the tumor has invaded a structure that cannot be operated upon without risking the patient's life. Occasionally surgery can improve survival even if not all tumor tissue has been removed; the procedure is referred to as "debulking" (i.e., reducing the overall amount of tumor tissue). Surgery is also used for the palliative treatment of some of cancers, e.g., to relieve biliary obstruction, or to relieve the problems associated with some cerebral tumors. The risks of surgery must be weighed against the benefits.

[0Θ1 9] Chemotherapy and radiotherapy are used as a first-line radical therapy in a number of malignancies. They are also used for adjuvant therapy, i.e. when the macroscopic tumor has already been completely removed surgically but there is a reasonable statistical risk that it recurs. Chemotherapy and radiotherapy are commonly used for palliation, where disease is clearly incurable: in this situation the aim is to improve the quality of life and to prolong it.

[00200] Hormone manipulation is well established, particularly in the treatment of breast and prostate cancer. There is currently a rapid expansion in the use of monoclonal antibody treatments, notably for lymphoma (Rituximab), and breast cancer (Trastuzumab).

[00201 J Useful anti-cancer agents include, but are not limited to, methotrexate, taxol, mercaptopurine, thioguanine, hydroxyurea, cytarabiiie, cyclophosphamide, ifosfamide, nitrosoureas, cisplatin, carboplatin, mitomycin, dacarbazine, procarbazine, etoposides, campathecins, bleomycin, doxorubicin, idarabicin, daunorubiein, dactinomyein, plicamycin, rnitoxantrone, asparaginase, vinblastine, vincristine, vinorelbine, paclitaxel, and docetaxel, gamma-radiation, alkylating agents including nitrogen mustard such as cyclophosphamide, Ifosfamide, trofosfamide, Chlorambucil, nitrosoureas such as carmustine (BCNU), and Lomustine (CC U), alkylsulphonates such as busulfan, and Treosulfan, triazenes such as Dacarbazine, platinum containing compounds such as Cisplatin and carboplatin, plant alkaloids including vinca alkaloids, vincristine, Vinblastine, Vindesine, and Vinorelbine, taxoids including paclitaxel, and Docetaxol, DNA topoisomerase inhibitors including Epipodophyilins such as etoposide, Teniposide, Topotecan, 9-aminocamptothecin, campto irinotecan, and crisnatol, mytomycins such as mytomycin C, and Mytomycin C, anti-metabolites, including anti-foiates such as DHFR inhibitors, methotrexate and Trimetrexate, IMP dehydrogenase inhibitors including mycopiienolic acid, Tiazofurin, Ribavirin, EICAR, Ribonuelotide reductase Inhibitors such as hydroxyurea, deferoxamine, pyrimidine analogs including uracil analogs 5-Fluoro racil, Floxuridine, Doxifluridine, and Ratitrexed, cytosiiie analogs such as cytarabine (ara C), cytosine arabinoside, and fludarabine, purine analogs such as mercaptopurine, thioguanine, hormonal therapies including receptor antagonists, the anti-estrogens Tamoxifen, Raloxifene and mcgestrol, LHRH agonists such as goscrclin, and Leuprolide acetate, anti-androgens such as flutamide, and bicalutamide, retinoids/deltoids, Vitamin D3 analogs including EB 1089, CB 1093, and H 1060, photodyamic therapies including vertoporfm (BPD-MA.), Phthalocyanine, photosensitizer Pc4, Demethoxy-bypocrellin A, (2BA-2-DMHA), cytokines including Interferon-. alpha,, Interferon-gamma, tumor necrosis factor, as well as other compounds having anti-tumor activity including Isoprenylation inhibitors such as Lovastatin, Dopaminergic neurotoxins such as I -methyl -4-phenylpyridinium ion, Cell cycle inhibitors such as staurosporine, Actinornycins such as Actinomycin D and Dactinomycm, Bleomycins such as bleomycin A2, Bleomycin B2, and Peplomycin, anthracyc lines such as daunorabicin, Doxorubicin (adriarnycin), Idarubicin, Epirubicin, Pirarubicin, Zorubicin, and Mitoxantrone, MDR inhibitors including verapamil, and Ca2+ ATPase inhibitors such as thapsigargin.

[0Θ202] Aspects of the invention relate to making a selection of a particular cancer therapeutic or anti-cancer agent or making a selection of a particular cancer therapy that relates to these cancer agents, which when administered to a patient, is preferably administered as component of a composition that optionally comprises a pharmaceutically acceptable vehicle. These compositions, which comprise a compound selected in the methods of the invention, are preferably administered orally. The compositions may also be administered by any other convenient route, for example, by infusion or bolus injection, by absorption through epithelial or mucocutaneous linings (e.g., oral mucosa, rectal, and intestinal mucosa, etc.) and may be administered together with another biologically active agent. Administration can be systemic or local. Various delivery systems are known, e.g., encapsulation in liposomes, microparticles, microcapsules, capsules, etc., and can be used to administer the compounds of the invention.

[0Θ203] Methods of administration of cancer agents that may be selected in methods of the invention include but are not limited to intradermal, intramuscular, intraperitoneal, intravenous, subcutaneous, intranasal, epidural, oral, sublingual, intranasal, intracerebral, mtravaginal, transdermal, reetally, by inhalation, or topically, particularly to the ears, nose, eyes, or skin. The mode of administration is left to the discretion of the practitioner. In most instances, admin stration results in the release of a compound selected by the methods of the invention into the bloodstream.

[00204 J in specific embodiments, it may be desirable to administer an anti-cancer compound locally. This may be achieved, for example, and not by way of limitation, by local infusion during surgery, topical application, e.g., in conjunction with a wound dressing after surgery, by injection, by means of a catheter, by means of a suppository, or by means of an implant, said implant being of a porous, non-porous, or gelatinous material, including membranes, such as sialastic membranes, or fibers,

[0Θ205] In certain embodiments, it may be desirable to introduce an anti-cancer compound into the central nervous system by any suitable route, including intraventricular, intrathecal and epidural injection. Intraventricular injection may be facilitated by an intraventricular catheter, for example, attached to a reservoir, such as an Ommaya reservoir.

[00206] Pulmonary administration can also be employed, e.g., by use of an inhaler or nebulizer, and formulation with an aerosolizing agent, or via perfusion in a fluorocarbon or synthetic pulmonary surfactant. In certain embodiments, the compounds can be formulated as a suppository, with traditional binders and vehicles such as triglycerides.

[00207 J In another embodiment, the compounds can be delivered in a vesicle, in particular a liposome (see Langer, 1990, Science 249: 1527-1533; Treat et al., in Liposomes in the Therapy of Infectious Disease and Cancer, Lopez-Berestein and Fidler (eds.), Liss, N.Y., pp. 353-365 (1989); Lopez-Berestein, ibid., pp. 317-327; see generally ibid.).

[00208] In yet another embodiment, the compounds that may be selected by methods of the invention can be delivered in a controlled release system (see, e.g., Goodson, in Medical Applications of Controlled Release, supra, vol. 2, pp. 1 15-138 (1984)). Other controlled-release systems discussed in the review by Langer, 1990, Science 249: 1527-1533) may be used. In one embodiment, a pump may be used (see Langer, supra; Sefton, 1987, CRC Crit. Ref. Biomed. Eng. 14:201; Buchwaid et al., 1980, Surgery 88:507 Saudek et al., 1989, N. Engl. J. Med. 321 :574). In another embodiment, polymeric materials can be used (see Medical Applications of Controlled Release, Langer and Wise (eds.), CRC Pres., Boca Raton, Fla. (1974); Controlled Drug Bioavailability, Drug Product Design and Performance, Smolen and Ball (eds.), Wiley, N.Y. (1984); Ranger and Peppas, 1983, J. Macromol. Sci. Rev. Macromol. Chem. 23:61; see also Levy et al, 1985, Science 228: 190; During et al, 1989, Ann. Neurol. 25:351; Howard et al., 1989, J. eurosurg. 71 : 105). In yet another embodiment, a controlled-release system can be placed in proximity of a target of a compound of the invention, e.g., a particular RNA, thus requiring only a fraction of the systemic dose.

[00209] The anti-cancer compound may optionally comprise a suitable amount of a pharmaceutically acceptable vehicle so as to provide the form for proper administration to the patient.

[00210] In a specific embodiment, the term "pharmaceutically acceptable" means approved by a regulatory agency of the Federal or a state government or listed in the U.S. Pharmacopeia or other generally recognized pharmacopeia for use in animals, mammals, and more particularly in humans. The term "vehicle" refers to a diluent, adjuvant, excipient, or carrier with which a compound of the invention is administered. Such pharmaceutical vehicles can be liquids, such as water and oils, including those of petroleum, animal, vegetable or synthetic origin, such as peanut oil, soybean oil, mineral oil, sesame oil and the like. The pharmaceutical vehicles can be saline, gum acacia, gelatin, starch paste, talc, keratin, colloidal silica, urea, and the like. In addition, auxiliary, stabilizing, thickening, lubricating and coloring agents may be used. When administered to a patient, the pharmaceutically acceptable vehicles are preferably sterile. Water is a preferred vehicle when the compound of the invention is administered intravenously. Saline solutions and aqueous dextrose and glycerol solutions can also be employed as liquid vehicles, particularly for injectable solutions. Suitable pharmaceutical vehicles also include excipients such as starch, glucose, lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel, sodium stearate, glycerol monostearate, talc, sodium chloride, dried skim milk, glycerol, propylene, glycol, water, ethanol and the like. The compositions, if desired, can also contain minor amounts of wetting or emulsifying agents, or pH buffering agents.

[00211] The compositions that may be selected by methods of the invention can take the form of solutions, suspensions, emulsion, tablets, pills, pellets, capsules, capsules containing liquids, powders, sustained-release formulations, suppositories, emulsions, aerosols, sprays, suspensions, or any other form suitable for use. In one embodiment, the pharmaceutically acceptable vehicle is a capsule (see e.g., U.S. Pat. No. 5,698,155). Other examples of suitable pharmaceutical vehicles are described in Remington's Pharmaceutical Sciences, Alfonso R. Gennaro ed., Mack Publishing Co. Easton, Pa., 19th ed., 1995, pp. 1447 to 1676, incorporated herein by reference.

[0Θ212] In a preferred embodiment, the compounds that may be selected by methods of the invention are formulated in accordance with routine procedures as a pharmaceutical composition adapted for oral administration to human beings. Compositions for oral delivery may be in the form of tablets, lozenges, aqueous or oily suspensions, granules, powders, emulsions, capsules, syrups, or elixirs, for example. Orally administered compositions may contain one or more agents, for example, sweetening agents such as fructose, aspartame or saccharin; flavoring agents such as peppermint, oil of wintergreen, or cherry; coloring agents; and preserving agents, to provide a pharmaceutically palatable preparation. Moreover, where in tablet or pill form, the compositions can be coated to delay disintegration and absorption in the gastrointestinal tract thereby providing a sustained action over an extended period of time. Selectively permeable membranes surrounding an osmotically active driving compound are also suitable for orally administered compositions. In these later platforms, fluid from the environment surrounding the capsule is imbibed by the driving compound, which swells to displace the agent or agent composition through an aperture. These delivery platforms can provide an essentially zero order delivery profile as opposed to the spiked profiles of immediate release formulations. A time delay material such as glycerol monostearate or glycerol stearate may also be used. Oral compositions can include standard vehicles such as mannitol, lactose, starch, magnesium stearate, sodium saccharine, cellulose, magnesium carbonate, etc. Such vehicles are preferably of pharmaceutical grade. Typically, compositions for intravenous administration comprise sterile isotonic aqueous buffer. Where necessary, the compositions may also include a solubilizing agent.

[00213] In another embodiment, the selected anti-cancer compound be formulated for intravenous administration. Compositions for intravenous administration may optionally include a local anesthetic such as lignocaine to lessen pain at the site of the injection. Generally, the ingredients are supplied either separately or mixed together in unit dosage form, for example, as a dry lyophilized powder or water free concentrate in a hermetically sealed container such as an ampoule or sachette indicating the quantity of active agent. Where the anti-cancer compounds are to be administered by infusion, they can be dispensed, for example, with an infusion bottle containing sterile pharmaceutical grade water or saline. Where the anti-cancer compounds are administered by injection, an ampoule of sterile water for injection or saline can be provided so that the ingredients may be mixed prior to administration.

[0Θ214] The amount of an anti-cancer compound that is effective in the treatment of a particular type of cancer depends on the nature of the disorder or condition, and can be determined by standard clinical techniques. In addition, in vitro or in vivo assays may optionally be employed to help identify optimal dosage ranges. The precise dose to be employed also depends on the route of administration, and the seriousness of the disease or disorder, and should be decided according to the judgment of the practitioner and each patient's circumstances. However, suitable dosage ranges for oral administration are generally about 0.001 milligram to about 200 milligrams of a compound of the invention or a pharmaceutically acceptable salt- thereof per kilogram body weight per day. In specific preferred embodiments of the invention, the oral dose is about 0.01 milligram to about 100 milligrams per kilogram body weight per day, more preferably about 0.1 milligram to about 75 milligrams per kilogram body weight per day, more preferably about 0.5 milligram to 5 milligrams per kilogram body weight per day. The dosage amounts described herein refer to total amounts administered; that is, if more than one compound is administered, or if a compound is administered with a therapeutic agent, then the preferred dosages correspond to the total amount administered. Oral compositions preferably contain about 10% to about 95% active ingredient by weight.

[0Θ215] Suitable dosage ranges for intravenous (i.v.) administration are about 0.01 milligram to about 100 milligrams per kilogram body weight per day, about 0.1 milligram to about 35 milligrams per kilogram body weight per day, and about 1 milligram to about 10 milligrams per kilogram body weight per day. Suitable dosage ranges for intranasal administration are generally about 0.01 pg kg body weight per day to about 1 mg/kg body weight per day. Suppositories generally contain about 0.01 milligram to about 50 milligrams of a compound of the invention per kilogram body weight per day and comprise active ingredient in the range of about 0.5% to about 10% by weight.

[00216] Recommended dosages for intradermal, intramuscular, intraperitoneal, subcutaneous, epidural, sublingual, intracerebral, intravaginal, transdermal administration or administration by inhalation are in the range of about 0.001 milligram to about 200 milligrams per kilogram of body weight per day. Suitable doses for topical administration are in the range of about 0.001 milligram to about 1 milligram, depending on the area of administration. Effective doses may be extrapolated from dose-response curves derived from in vitro or animal model test systems. Such animal models and systems are well known in the art.

[0Θ217] Methods of the invention also comprehend selection of cancer agents that may be provided in pharmaceutical packs or kits comprising one or more vessels containing the cancer agent. Optionally associated with such container(s) can be a notice in the form prescribed by a governmental agency regulating the manufacture, use or sale of pharmaceuticals or biological products, which notice reflects approval by the agency of manufacture, use or sale for human administration. In a certain embodiment, the kit contains more than one compound of the invention. In another embodiment, the kit comprises a therapeutic agent and a compound of the invention.

[00218] The compounds that may be selected by methods of the invention are preferably assayed in vitro and in vivo, for the desired therapeutic or prophylactic activity, prior to use in humans. For example, in vitro assays can be used to determine whether it is preferable to administer a compound alone or in combination with another compound of the invention and/or a therapeutic agent. Animal model systems can be used to demonstrate safety and efficacy.

[00219] Other methods are known to the skilled artisan and are within the scope of the invention.

[00220] Table 1 shows a tabulation of 99 FFPE samples of different ages and their characteristics that DNA was extracted from to determine if production scale WES could be applied to FFPE-derived sample.

Block

Block

Block

Table 2 shows a tabulation of the levels of evidence. To assign the strictest possible definition of evidence linking an alteration to a clinical action for each given variant, ail highest scoring variants are curated with the aim of assigning each a level (A through E) depending on the category of action. Inferential associations are based on homology, computational data, structural information, or pathway involvement. Those that not meet criteria for any level evidence are considered unknown variants.

diagnosis [00222] Table 3 shows a first section of data associated with 41 clinically relevant alterations in 15 out of 16 patients.

[00223 J Table 4 shows a second section of c ata associated with ^{L ■}1 clinically relevant alterations in 15 out of 16 patients.

Tumor

Tumor

[00224] Table 5 shows a third section of data associated wit 41 clinically relevant alterations in 15 out of 16 patients.

DFCI.1 1 - Bialielic inactivation or mutation may^¬ 1 17 7576858 7576858

] 04.04-Tumor be prognostic in some tumor types.

They may also predict sensitivity to

some cell cycle inhibitors and p53

specific gene therapies or

immunotherapies. May signal the

presence of a germline mutation.

DFCL l l - Some prognostic effects in colon 1 3 41266097 41266097 104.05-Tumor cancer and gastric cancer. Activation

may mediate resistance to EGFR

TKLs, PI3K inhibitors, and AKT

inhibitors. Activation may predict

sensitivity to inhibitors of WNT

signaling

DFCL 1 - Mutations may predict sensitivity to 1 178916876 178916876 104.05-Tumor P13K pathway inhibitors -- P13K

inhibitors, AKT inhibitors, and

MTOR inhibitors. Mutations may

predict resistance to anti-RTK

therapy, including cetuximab, anti- EGFR TK Is. and trastuzumab and

lapatinib

DFCL l l - Amplification may result in resistance 0 22 21242126 21386103 104.06-Tunior to EGFR inhibition and RAF

inhibition. Amplification may predict

sensitivity to SRC inhibitors.

DFCI.1 1 - Bialielic inactivation or mutation may^¬ 1 17 7578213 7578214

104.06-Tumor be prognostic in some tumor types.

They may also predict sensitivity to

some cell cycle inhibitors and p53

specific gene therapies or

immunotherapies. May signal the

presence of a germline mutation.

DFCL l l - Bialielic inactivation or mutation may 0 17 7573010 7579592 104.07-Tumor be prognostic in some tumor types.

They may also predict sensitivity to

some cell cycle inhibitors and p53

specific gene therapies or

immunotherapies. May signal the

presence of a germline mutation.

DFCI.1 1 - Mutations targetable with TK s (both 0.75 55259515 55259515 104.08-Tumor FDA approved and novel). Other

mutations predict resistance to TKIs.

Amplification associated with

response to anti-EGFR Abs in colon

cancer. Amplification also associated

with resistance to TKIs in some cancers, Rearangement is prognostic

in GBM, H SCC

DFCL l l - Biallelic mactivation or mutation may 2 17 7579315 757931 5 104.08-Tumor be prognostic in some tumor types.

They may also predict sensitivity to

some cell cycle inhibitors and p53

specific gene therapies or

immunotherapies. May signal the

presence of a gerniline mutation.

DFCI.1 1 - May be prognostic or diagnostic in 0 13 48830521 51 826339 104.09 POST some tumor types. Loss may predict

resistance to CDK inhibitors.

DFCI.1 1 - Mutations targetable with TKIs (both 7 55272966 55272966 104.1 1 -Tumor FDA approved and novel). Other

mutations predict resistance to TKIs.

Amplification associated with

response to anti-EGFR Abs in colon

cancer. Amplification also associated

with resistance to TKIs in some

cancers. Rearangement is prognostic

in GBM, HNSCC

DFCI.1 1 - Diagnostic in prostate cancer 2 12 12022819 12022819 104.1 1 -Tumor

DFCL l l - Amplification may predict sensitivity 0 12 68052495 70087689 104.1 1 -Tumor to Nutlins and MDM2 inhibitors

DFCI.1 1 - Deletion is prognostic in GBM 14 35872052 35872053

104.1 1 -Tumor

DFCI.1 1 - Amplification may predict resistance 0 X 66766606 68836550 104.13-Tumor to androgen deprivation in prostate

cancer and may predict sensitivity to

second generation androgen

deprivation or direct androgen

inhibitors

DFCI.1 1 - Amplification may predict resistance 2 X 66765243 66765245 104.13-Tumor to androgen deprivation in prostate

cancer and may predict sensitivity to

second generation androgen

deprivation or direct androgen

inhibitors

DFCI.1 1 - Biallelic mactivation or mutation may 1 17 7577559 7577559 104.13-Tumor be prognostic in some tumor types.

They may also predict sensitivity to

some cell cycle inhibitors and p53

specific gene therapies or

immunotherapies. May signal the presence of a germline mutation.

M-l 1 -001 -3- Mutations predict sensitivity to RAF -0.25 140453136 140453136

Tumor inhibitors. Amplification may predict

⁷

resistance to MEK inhibitors.

M-l 1 -001 -3 - Mutations may predict sensitivity to 1.75 9 212426678 212426678 Tumor Lapatinib and other anti-EGF family

inhibitors

M-l 1 -001 -3- Mutations may be diagnostic of 20 57415501 57415501 Tumor tumors arising in McCune -Albright

syndrome, and may be targetable with

JAK inhibitors

M-l 1 -001 -3- Mutations predict resistance to RAF- 0 15 66727451 66727451 Tumor and MEK- inhibitor

M-l 1 -001 -3- Biallelic inactivation may predict 0 10 89463521 89624307

Tumor sensitivity to PI3K pathway inhibitors

- PI3K inhibitors, AKT inhibitors,

and MTOR inhibitors. Biallelic

inactivation may predict resistance to

anti-RTK therapy, including

cetuximab, anti-EGFR TKIs, and

trastuzumab and lapatinib. Biallelic

inactivation may predict sensitivity to

PART inhibitors

Nerve Sheath Biallelic inactivation may predict 0 9 21816773 22451912 hgl9-Tumor sensitivity to CDK4/6 inhibitors.

Nerve Sheath Biallelic inactivation may predict 0 9 21 816773 22451912 hg 19 -Tumor sensitivity to CDK4/6 inhibitors.

Nerve Sheath Activating mutations may predict 1 11227530 1 1227530 hgl9-Tumor sensitivity to MTOR inhibitors.

Secondary mutations may predict

resistance to MTOR inhibitors

Nen'e Sheath Inactivation may predict sensitivity to 1 22 24133967 24133967 hg 19 -Tumor CDK Inhibitors, Hedgehog Inhibitors,

and/or HD AC inhibitors

Nerve Sheath Inactivation may predict sensitivity to 2 22 24167563 24167563 hgl9-Tumor CDK Inhibitors, Hedgehog Inhibitors,

and/or HDAC Inhibitors

Osteosarcoma Mutations may predict sensitivity to 0 178936093 178936093 hg 19 -Tumor PI3K pathway inhibitors - PI3K

inhibitors, AKT inhibitors, and

MTOR inhibitors. Mutations may

predict resistance to anti-RTK

therapy, including cetuximab, anti- EGFR TKIs, and trastuzumab and la atiiiib

Osteosarcoma Biallelic inactivation or mutation may^¬ 1 17 7577538 7577538 hg 9 -Tumor be prognostic in some tumor types.

They may also predict sensitivity to

some cell cycle inhibitors and p53

specific gene therapies or

immunotherapies. May signal the

presence of a germline mutation.

pat2 Amplification may predict sensitivity 0 12 58109755 58223381

Glioblastoma- to CDK4/6 inhibitors.

Tumor

pat2 Mutations targetable with TKIs (both 0 4 52744022 57273884

Glioblastoma- FDA approved and novel). Secondary

Tumor mutations predict resistance to TKIs.

Amplification also associated with

resistance to TKIs.

pa†.2 Alterations may predict sensitivity to 2 4 55133621 55133621

Glioblastoma- imatinib and other TKIs

Tumor

Unknown Biallelic inactivation may predict 0 9 20346574 22029516 Primary 04- sensitivity to CDK4/6 inhibitors.

Tumor

Unknown Biallelic inactivation may predict 0 9 20346574 22029516 Primary 04- sensitivity to CDK4/6 inhibitors.

Tumor

Unknown Alterations may predict sensitivity to 1 .75 10 123256162 123256162 Primary 04- FGF inhibitors

Tumor

Unknown Biallelic inactivation or mutation may 1 17 7577550 7577550 Primary 04- be prognostic in some tumor types.

Tumor They may also predict sensitivity to

some cell cycle inhibitors and p53

specific gene therapies or

immunotherapies. May signal the

presence of a germline mutation.

[00225] Table 6 shows a fourth section of c ata associated wit l 41 clinically relevant alterations in 15 out of 16 patients.

Tumor

Osteosarcoma hgl9- T C 79 0.53

Tumor

pai2 Glioblastoma- NA NA NA NA

Tumor

pat2 Glioblastoma- NA NA NA NA

Tumor

pat2 Glioblastoma- T G 609 0.76

Tumor

Unknown Primary 04- NA NA NA NA

Tumor

Unknown Primary 04- NA NA NA NA

Tumor

Unknown Primary 04- A C 156 0.04

Tumor

Unknown Primary 04- G C 105 0.50

Tumor

Table 7 shows a fifth section of data associated with 41 clinically relevant alterations in 15 out of 16

0fs* 15(l) on with ΗίΡΚΊ (By

similarity). |In teraction with

CARMl . Inte faction with H1PK2,

!)!·(·: ! ! · NA A p.D32Y(l 10)|p.A5 A80del( 3166

104.05-Tumor 63)ip,D32N(58)|p,D32G(53)

!p,D32H(37)!p,D32V(20)!p,

D32Af 12)!p.H24 847dei(9)j

p.A5 A80>D(7)|p.A5 Q143

del(7)ip.\VOQQSYLD25?(5

)|p.Q28 H134del(5)|p.W25

D32del(4)|p.W25 I140del(4

)!p.S23 S33del(3)|p.V22 G

38del(3)!p.T3 A 126del(2) jp.

M5 N141 >D(2)ip.D32E(2)|

p.D32 S47del(2)jp.W25 H3

6del(2)|p.Y30 S33del(2)|p.

V22 S33del(2)|p.V22 L139

>V(2)!p.A5 Yi 42>Df 2) jp. A

5fs*7(2)|p.?(2)ip.LiO N141

del(2)ip.D6 A43del( 1 )jp.E9

S47del(l )|p.Q28 Q61 del(l

)|p.A20 151del(l)|p.A20

N141del(l)!p.Dl l Y142>H(

l)|p.H24 G38del(T)!p.S29

H36del( 1 )jp.Y30 A97del( i)j

p.A20 A80de](l)!p.Q28 A4

3 del( 1 ) p.E 15 1140>V( 1 ) |p .

D17 P128del(l)jp,H24 Ml

31del(l)!p,L7 I140del(Y)|p.

K19 Y142>V(l)!p.A2() LI

48del(1 )|p.V22 A80del(!)jp.

W25 I35def(l)|p.V22 G80>

NNNNN(l )|p.A5 5del(l)i

P.A20 0143del(l)!p.A13

151dei(i)|p.D32del(l)jp.S23

I140del(l )|p.Ml A87del(l

)!p.W25 S33del(1 )!p.V22 T

102del( 1 ) |p. S23 A39del( )!

P.A21 A80del(l)|p,D6 1140

dei(l )ip.Q28 H40del(l)|p,E

9 A80dei(l )!p.M14 S45del(

l )|p.M8 G50del(l )jp.A5 G

80>(l)!p.D32 H36>D(l)|p.P

16 K133del(l )|pA5 T59del

(l)ip.A20 I35del( l)jp.Ml V 173dei(l)jp.A5 R90dei(l)|p.

V22 Y64del(l)ip.M8 A80d

ei(l)|p.E9 I140del(l)jp.D32

S33insS(i)|p.Y30 T4()del(

i)|p.Ml T42del(l)|p.A5 Ql

43>E(l)ip.A5 Q72del(l )|p.

Q28 D32>H(l)ip.Y30 A80

del(l)ip.D32fs*9( )|p.D6 K

133dei(l)|p.A5 T42del(l)|p.

A5 D144>D(l)jp.A5 T40de

l(i)[p.D17 Ai26dei(l)|p.A5

E54dei(l)|p.S23 T35del(l)|

p.V22 S71>A(l)|p.W25 A8

0del(l)|p.A20 Q72dei(l)jp.

A20 Sllldel(l)ip.D32 H36

d l;! !

DFCI.11- NA NA p.R88Q(26) 3553 PI3K-ABD. 104.05-Tumor

DFCL11- 33 3.3003 NA NA NA

104.06-Tumor

DFCI.11- NA NA p.F212fs*3(7)|p.0?(7)|p.F21 22245 Required for

104.06-Tumor 2L(3)|p.F2] 2S(2)ip.F2121(2) interaction

!p.D208fs*l(l)jp.T211 F21 with

2insX(l)|p.R209 R213delR FBX042.|!Ini NTFR(] )|p.D20 ^" R2i3delD eraction with DRNTFR(l)|p.T2l 1 fs*28(l) ΗΓΡΚΊ (By !p.T211 S2I5deiTFRHS(l) similarity), in p.Kl 64 P219de{{l)|p.D207 teraction V216dellO(l)|p.F212fs*4(l) withAXlNl !p.F212Y(l)!p.R209f *6(l)|p (By

.D208 V216delDRNTFRH similarity). SV(!)

DFCL11- 5 -2.31485 NA NA NA

104.07-Tumor

DFC^'1.11- A NA p.L858R(3429)!p.L858Li4)i 9571 Cytoplasmic 104.08 -Tumor p.L858M(4)|p.L8580(3)!p.L (Potential). !P

858 A( 2 ) 1 p , L 858 W( 1 ) . L 858 rotein kinase. P(l)|p.L858K(i)jp.L858G(l)

DFCI.11- NA NA p.0?(7)|p.C124R(4)|p.G59fs 22245 Required for 104.08-Tumor *23 (3) |p. C 124fs*46(2) |p. C 1 interaction

24G(!)ip.V73fs*9(l)|p.C124 with fs*0(l ) .GlOS T125del21 ( FBX042.jjlnt l)|p.Y107fs*44(l)|p.T125fs eraction with *24(l)|p.C124S(l)!p.P13fs* HIPK1 (By 18(1) !p. S33 fs*23( 1 ) jp.C 124f similarity). In s*48(l)!p.C124Y(l)ip.C124f teracti n s*25(l) with ΑΧ1ΝΊ (By

similarity).

!)!·(·: ! ! · 121 -1.072 NA NA NA

104,09 POST

DFCI.1 1- NA NA 9571 Cytoplasmic 104.1 1 -Tumor (Potential).

DFCI.1 1- NA NA 250

104. ^"11 -Tumor

DFCI. l l- 106 2.0052 NA NA NA

104.1 1 -Tumor

DFCI.1 1 - NA NA 2 ANK 4.

104.11 -Tumor

!)!·(·: ! ! · 17 5.0875 NA NA NA

04.13 -Tumor

DFCI.1 1 - A NA 8 Poly-

104.13 -Tumor Gln.jModulat ing. Gin-rich.

DFCI. l l- NA NA p.S241F(73)|p.S241C(24)|p. 22245 Interaction

104.13-Tumor S241 fs*6(8)|p.0?(7)|p.S241 with HIPK1

Y(7)|p.C242fs*5(6)ip.S24I A (By

(6) ip . S241 del(5) |p. S241 T(5) | similarity). In p.N239 C242delNSSC(3)|p. teracts with S241 S(3)jp.S241P(3)|p.S241 the 53BP2 fs*22(2)!p.Y236 M243deiY SH3 MCNSSCM( 1 ) ip.N239fs*4( domain. Inter 1 )|p.C238 M246delC^"NSSC action with MGGM( ) |p . S241 C242ins AXIN1 (By- X(l)|p.S241 G245delSCM similarity) . GG(i)!p.C238fs*21(l)|p.S24

ifs*7(l )ip.H233 C242del^"10

(l )ip.^"N239 C242>S(l)|p.S2

41 fs*23(l jp,N239 C242del

(1)

M- 11 -001 -3- NA NA NA p.V600E(168 Tumor 92)!p.V600?(

325)|p.V600

K(176)!p.V6

00R(36)!p.V

T(3)!p.T599

R603>l(2)|p. T599 V600> IAL(2)|p.V6 00L(2)|p.T59 9 V600insT( 2)!p.V600 W

604del(l)|p.

V600 S605> DV( l)|p.V60 0 S605>D(1 )|p.T599_V6 00insV(l)|p. T599 V600i nsDFGLAT( 1 )

M-l 1-001-3- NA NA NA

Tumor

M-l 1 -001-3- NA NA NA

Tumor

M-l 1-001 -3- NA NA NA

Tumor

M-l 1 -001-3- 21 -1.8793 FALSE NA

Tumor

Nerve Sheath 11 -1.1594 NA NA NA hgl9-Tumor

Nerve Sheath 11 -1.1594 NA NA NA hgl 9-Tumor

Nerve Sheath NA NA 29 FAT.

hgl9-Turnor

Nerve Sheath NA NA p.R40*(10)|p.?(2)|p.L36fs*l 407

hgl 9-Tumor 3(l)|p.R40fs*15(l)

Nerve Sheath NA A p.?(6)lp ί ?66 *386del(l) 407 Interact on hgl9-Tumor with

PPP1 15A, 2.|2 X approximate tandem repeats.

Osteosarcoma A NA p.E545K(735)|p.E545A(75)| 3553 P13 helical. hgl9-Tumor p.E545G(55)|p.E545?(19)ip.

E545D(15)jp.E545Q(12)!p.E

545V(4)

Osteosarcoma NA NA p.R248Q(523)|p.R248W(44 22245 Interaction hgl9-Tumor 3)|p.R248L(63)ip.R248P(12) with HTPK.1

!p.R248G(l l )|p.R248R{10)i (By p.0?(7 |p.R155Q(4)|p.N247 similarity). In R248delNR(2)|p.N247 R24 teracts with

8>KW(2)|p.M246 P250del the 53BP2 MNRRP(2)jp.R248fs*97(2)j SH3 p.R248 P250delRRP(l } jp.N domain. Inter 247 R249delNRR{l)|p.N24 action with 7 P250delNRRP( l)jp.R249f AXIN1 (By s*96(l)|p.R248C(l)|p.G245f similarity). s* 14(l)!p.N247__R248>IP(l )

pat2 59 4.3814 NA NA NA

Glioblastoma- Tunior

pat2 194 2.6432 NA NA NA

Glioblastoma- Tumor

pat2 NA NA 674 Extracellular

Glioblasioma- (Potential). Tumor

Unknown 73 -1.0728 NA NA NA

Primary 04- Tumor

Unknown 73 -1.0728 NA NA NA

Primary 04- Tumor

Unknown NA NA 96 Cytoplasmic Primary 04- (Potential).!? Tumor rotein kinase.

Unknown NA NA p.G244S(35)|p.G244C(34)|p 22245 Interaction Primary 04- . G244DC32) |p.G244 V( 14)| . with HlP l Tumor G244G(13)!p.G244A{9}!p.0? (By

(7)ip.G244fs*3(5)|p.G244R( similarity). In 3)|p.M243 G244>IC(l )|p.G teracts with 2441s* 19(i)!p.G244fs* 17{1) the 53BP2 !p.M243 fs* 18( i ) \p. G244E( 1 SH3

) jp. S241 G245delSCMGG( domain. Inter l )!p.C242fs*98(l)|p.C242 action with M246>L( 1 ) ip. G244del( 1 ) !p . AXINl (By C238 M246delCNSSCMG similarity). GM(1)

[00227 J A sample alteration report. Each alteration nominated by PHIAL is curated to answer specific fields that are intended to guide physician interpretation.

Patieiii ID DFCI..J 1-104.03

Tumor Type Lung Adenocarcinoma

[00228] Sequencing issues

[00229] Gene Description (Brief Introduction to this gene): Activating mutations in KRAS are among the most common genetic alterations in human tumors. KRAS mutations play a central role in tumor progression in multiple cancer types, and have been implicated in poor prognosis and resistance to therapy.

[00230] Gene Frequency (Incidence of alterations in the gene in cancer overall and in this cancer in particular): KRAS alterations are common across numerous malignancies. KRAS mutations are the most common molecular change found in NSCLC. Activating KRAS mutations are found in 20-30% of all patients with lung adenocarcinoma. In TCGA, 25% of lung adenocarcinomas were found to have KRAS mutations (cBio, April 2013).

[00231] Alteration Function (function of this alteration (activating, likely activating, inactivating, likely inactivating, iinknown/iincharacterized) and rationale): This alteration is a known activating mutation, though may be less potent than the more common codon 12 and 13 mutations (PMID: 20570890).

[00232] Alteration Frequency in this tumor type: This specific alteration has not been previously reported in lung adenocarcinoma. A single patient with lung adenocarcinoma patient was found to have a KRAS A146P mutation (COSMIC, April 2013). A146 mutations in KRAS were not found in 2 studies comprised 449 cases of NSCLC in which KRAS was sequenced in its entirety (PMID: 18948947, 18632602). More than 90% of KRAS mutations in lung cancer are codon 12 mutations.

[0Θ233] Alteration Frequency in other tumor types (if uncommon in this tumor type): This alteration has rare!)' been found in other cancer types. This alteration has only been reported in 15 colorectal cancer cases in the COSMIC database. An additional 68 cases of A146T have been reported in colorectal cancer in the COSMIC database. However, one systematic study of exon 4 mutations in colorectal cancer demonstrated the presence of A 146 mutations in 5% of colon cancers (PMID: 20570890).

[00234] Prognostic implications (prognostic implications of this alteration and/or of this functional change (activation, loss, etc) in this tumor type, with evidence/rationale.): Activating mutations in KRAS have been shown to be associated with a poor prognosis in NSCLC (Reviewed in PMID: 23401440), though these studies have generally only included codon 12 and 13 mutations.

[0Θ235] Diagnostic implications (diagnostic implications of this alteration and/or of this functional change (activation, loss, etc) in this tumor type, with evidence/rationale. ): None.

[0Θ236] Therapeutic implications (therapeutic implications (sensitivity and resistance) of this alteration and/or of this functional change (activation, loss, etc) in this tumor type, with evidence/rationale.): Activating KRA mutations may predict resistance to anti— EGFR therapies, which are FDA— approved for use in lung adenocarcinoma (Reviewed in PMID: 23401440). Many clinical trials of novel therapeutic agents have been designed specifically for use in KRAS— mutant lung adenocarcinoma (Reviewed in PMID: 23401440). Because activating mutations in KRAS may predict sensitivity to inhibitors of the RAS/RAF/MEK/ERK pathway, many of these trials focus on specific targeting of the M AP— kinase pathway (especially MEK). Preclinical studies have shown that MEK inhibitors, in particular, may be effective for KRAS mutant tumors, and these agents are in clinical trials for patients with KRAS mutant cancers. A. recent randomized phase II study of selumetinib (AZD6244) in combination with docetaxel versus docetaxel alone demonstrated an improved PFS in patients with KRAS— mutant, locally advanced, or metastatic NSCLC (PM ID: 23200175). However, the parallel mouse lung cancer co— clinical trial suggests that concomitant loss of STK1 1 with activating mutations in KRAS may confer primary resistance to combination therapy with docetaxel and the MEK inhibitor selumetinib ( AZD6244), possibly through activation of parallel signaling pathways such as AKT and SRC (PMID: 22425996). In addition to selumetinib, several other MEKinhibitors are also in clinical development including trametinib (GSK1 120212), GDC-0973, MEK 162, and pimasertib (AS703026 or MSC1936369B). Based on preclinical data, therapies targeting the PBK/AKT/mTOR pathway are also being investigated in KRAS-mutant lung cancers (Reviewed in PMID: 23401440). Data from preclinical KRAS-mutant, genetically engineered mouse models of NSCLC suggest that dual inhibition of the PI3K and MEK pathways are required, and clinical trials of this combination are underway. Other agents that are being studied in KRAS mutant lung cancers include HSP90 inhibitors (PMID: 23012248). There is preclinical evidence data implicating a synthetic lethal relationship between activated KRAS and CDK440 (PMID: 20609353). Finally, recent clinical data suggests a synthetical lethal interaction of the combination of MEK inhibitors and the BCL-XL inhibitor ABT-263 (navitoclax) in KRAS mutant cancers (PMID: 23245996). Examples of ongoing clinical trials for KRAS -mutant lung cancers include trials of MEK inhibitors (NCT00890825, NCT01362296). MEK mhibitors + PI3K mhibitors (NCTO 1449058), MEK inhibitors + RAF mhibitors (NCTO 1352273), MEK inhibitors + EGFR inhibitors (NCTO 1229150), MEK inhibitors + IGFl-R inhibitors (NCTO 1562899), Bortezomib (NCT01833143), HSP90 mhibitors (NCT01427946, CTO 1348126) and others (clinicaltrials.gov, April 2013 ). (Therapies in Clinical Trials, LEVEL [00237] A).

[00238] Categorization and Levels of Evidence:

CATEGORY: LEVEL A LEVEL B LEVEL C LEVEL D LEVEL E

Predictive—

FDA-

Resistance to eriotinib

approved

therapies

3V9EK inhi itors

P13 inhibitors

CDK inhibitors

Predictive -- RAF inhibitors

Theraptes Srt !GFI -R inhibitors

BCL-XL * MEK

ciirticaE trials Bortezomib

inhibitors

HSP90 inhibitors

Combinations

Negative Prognostic

rognostic

Diagnostic

Sequencing Issues: None.

[00240] Gene Description (Brief Introduction to this gene): STKl 1 is a well-known tumor suppressor (also known as LKB l) that is commonly inactivated in several cancers. Germline mutations in STK11 cause Puetz-Jeghers Syndrome (PJS).

[00241] Gene Frequency (Incidence of alterations in the gene in cancer overall and in this cancer in particular): STKl 1 is mutated in 15-20% of patients with lung adenocarcinoma. It is commonly seen in conjunction with KRAS mutations. In TCGA, 15% of lung adenocarcinomas were found to have STK l 1 mutations or deletions (cBio, April 2013).

[0Θ242] Alteration Function (function of this alteration (activating, likely activating, inactivating, likely inactivating, unknown/uncharacterized) and rationale): This alteration is likely inactivating, as it is a frameshift mutation that occurs at codon 279 out of 434.

[00243 J Alteration Frequency in this tumor type: This specific alteration has not been reported in the COSMIC database for NSCLC, though inactivating mutations in STKl 1 are common in this tumor type, occurring at a rate of 5-20% of NSCLC. They commonly co-occur with KRA S mutations.

[00244] Alteration Frequency in other tumor types (if uncommon in this tumor type): N/A

[00245 J Prognostic implications (prognostic implications of this alteration and/or of this functional change (activation, loss, etc) in this tumor type, with evidence/rationale.): Unknown.

[00246] Diagnostic implications (diagnostic implications of this alteration and/or of this functional change (activation, loss, etc) in this tumor type, with evidence/rationale.): None.

[00247] Therapeutic implications (therapeutic implications (sensitivity and resistance) of this alteration and/or of this functional change (activation, loss, etc) in this tumor type, with evidence/rationale.): Loss of STK11 activates the MTOR pathway and therefore may predict sensitivity to inhibitors of this pathway. Preclinical evidence suggests that MTOR inhibitors are effective in cancers with STKl 1 loss, and there is at least 1 case report of a pancreatic cancer with STKl ! loss with a response to an MTOR inhibitor (PM ID 21 189378, Level C). A clinical trial of everolimus in PJS patients with advanced cancer is now underway. In lung cancer, preclinical evidence suggests that PI3K MTOR inhibition may be effective specifically in STKl 1/KRAS mutant lung cancers (PMID: 21998291). A recent mouse lung cancer co-clinical trial suggests that concomitant loss of STK11 with activating mutations in KRAS may confer primary resistance to combination therapy with docetaxel and the MEK-inhibitor selumetinib (AZD6244), possibly through activation of parallel signaling pathways such as AKT and SRC (PMID: 22425996). However, a recent study presented at the AACR 2013 annual meeting demonstrated conflicting results, showing that cancer cell lines with STKl 1 loss were sensitive to MEK inhibition, ("LKB1 loss leads to activation of the CREB transcription factor and sensitivity to MEK inhibition in human lung cancer", Kaufman and Carbone, AACR 2013 Annual Meeting). Another preclinical study showed that SRC and FAK kinases are activated in ST 11 -deficient primary and metastatic lung tumors, and these cells are sensitive to the SRC- inhibitor dasatinib and/or the FAK inhibitor PF573228 (PMID: 20541700), Moreover,! be addition of dasatinib restored sensitivity of mouse tumors to the combination of PDK + MEKl/2 inhibitors, which are effective in KRAS mutant mouse tumors but not in KRAS/^'STKl 1 mutant mouse tumors. A recent preclinical study identified phenformin, a mitochondrial inhibitor and analog of the diabetes therapeutic metformin, as selectively inducing apoptosis in LKB1- deficient NSCLC cells. Therapeutic trials in mouse models of NSCLC revealed that tumors with Kras and Lkb l mutations, but not those with Kras and p53 mutations, showed selective response to phenformin as a single agent, resulting in prolonged survival (PM ID: 23352126). A clinical trial of metformin in lung cancer is currently underway (NCT01578551).

[00248] Categorization and Levels of Evidence:

CATEGORY: LEVEL A LEVEL B LEVEL C LEVEL D LEVEL E

Predictive—

FDA- approved Temsira!imus

therapies

Sv3£K inhibitors

P13K inhibitors

Predictive - MOTORS inhibitors

Thsrs ies irt SRC inhibitors

clinicai trials FAK inhibitors

Metformin

Combinations

Prog nostsc

Diagnostic

Gene ATM

Alteration

Patient ID IXFCL1 UR03

Tumor Type Lung Adenocarcinoma

[00249] Sequencing: Issues None. [00250] Gene Description (Brief introduction to this gene): ATM is a known tumor suppressor and has been implicated in multiple cancer types. Germline mutations in ATM cause Ataxia Telangiectasia,

[00251] Gene Frequency (Incidence of alterations in the gene in cancer overall and in this cancer in particular): ATM inactivation is common and has been implicated in multiple cancer types.

[00252] Alteration Function (function of this alteration (activating, likely activating, inactivating, likely inactivating, unknown/uncharaeterized) and rationale): This alteration is likely inactivating, as it is a frameshift mutation that occurs at codon 208 out of 3057.

[00253] Alteration Frequency in this tumor type: This specific alteration has not been reported in the COSMIC database for NSCLC, though inactivating mutations in ATM have been reported in this tumor type.

[00254] Alteration Frequency in other tumor types (if uncommon in this tumor type): This specific alteration has not been reported in the COSMIC database for other cancers, though inactivating mutations in ATM are common in several tumors, especially lymphoid tumors such as mantle cell lymphoma and CLL.

[00255] Prognostic implications (prognostic implications of this alteration and/or of this functional change (activation, loss, etc) in this tumor type, with evidence/rationale.): N/A

[00256] Diagnostic implications (diagnostic implications of this alteration and/or of this functional change (activation, loss, etc) in this tumor type, with evidence/rationale.): None.

[00257] Therapeutic implications (therapeutic implications (sensitivity and resistance) of this alteration and/or of this functional change (activation, loss, etc) in this tumor type, with evidence/rationale.): Inactivation of ATM may predict sensitivity to PARP mhibitors. Preclinical evidence from cell culture and mouse xenograft models demonstrated that ATM-deficient lymphoid tumor cells were sensitive to PARP inhibition (PMID: 22416035). A clinical trial of the PARP inhibitor olaparib that enrolled patients with ATM-deficient gastric cancer was recently completed.

[00258] Categorization and Levels of Evidence: CATEGORY: LEVEL A LEVEL B LEVEL C LEVEL D LEVEL B

FDA- approved

therapies

Predictive - Therapies in PARP inhibitors

clinical trials

Prognostic

Diagnostic

[0Θ259] Supplementary Table 1. Raw sequencing metrics for 868 samples. HS Metrics data for 868 samples are provided in this table, including data on 99 FFPE samples. Additional details on data represented by columns are provided at the following URL: hitp://picard.sourceforge.nei/pica^

Penalty

Starting Target 20x of

Tumor material Input Bases EXEX % Normal type Vol Cone DNA (ng) T^Jond Pico Catch Pico 20% data Adapter2 Normal Fresh 109 2.4132 120.66 68.72770626 8.865047797 92.25 4.46 0.0053

Frozen

Tissue

3 Tumor Fresh 109 2.62921 131.4605 63.90876551 9.201963562 89.25 5.22 0.0143

Frozen

Tissue

4 Tumor Fresh 109 2.45301 122.6505 64.71992915 9.040420913 91.43 4.87 0.0124

Frozen

Tissue

5 Normal Fresh 109 2.91108 145,554 61,75411209 8.968881599 92,47 4.43 0.0116

Frozen

Tissue

6 Tumor Fresh. 109 2.58408 129.204 40.71152961 9.04nw83 90.69 5.47 0.0033

Frozen

Tissue

? Norma! Fresh 109 2.55894 127.947 49.79029709 8.467228839 91.96 4.87 0.0029

Frozen

Tissue

8 Normal Fresh 109 2.52082 126,041 48,20073515 8.20617002 91,36 4.73 0.0051

Frozen

Tissue

9 Tumor Fresh 109 2.58856 129.428 73.19478854 8.802600085 91.47 5.07 0.0043

Frozen

Tissue

0 Normal Whole 109 2.7102 135.51 62.31746937 8.625331423 91.39 4.55 0.0065

Blood

1 Normal Whole 109 2.94475 147.2375 64.35607886 10.22001222 92.23 4.53 0.0066

Blood

2 Tumor Fresh 109 2.87712 143.856 74,83301882 8.300806913 90.87 5.33 0.0048

Frozen

Tissue

3 Tumor Fresh 109 2.57908 128.954 68.90610765 9.208352254 90.04 5.12 0.0061

Frozen

Tissue

4 Tumor Fresh 109 2.72359 136.0795 67.9291986 9.814119639 89.73 5.64 0.0037

Frozen

Tissue

5 Tumor Fresh 109 2.89413 144,7065 68.24626234 8.980254876 89.6 5.51 0.0034

Frozen

Tissue

6 Tumor Fresh 109 2.95504 147.752 63.42842853 8.492924019 91.31 5.07 0.003

Frozen

Tissue

7 Normal Fresh 109 2.94995 147.4975 74.94445051 8.728043939 91.58 4.5 0.0061

Frozen

Tissue

8 Normal Whole- 109 2.05681 102.8405 69.39526323 8.619504374 91.3 4.55 0.0051

Blood

9 Tumor Fresh 109 2.48351 124.1755 33.20494 14 8.393758877 92.83 4,56 0.0079

Frozen

Tissue

0 Tumor Fresh 109 1.73556 86.778 32.5457271 9.106659717 92.08 4.63 0.0074

Frozen

Tissue

1 Normal Fresh 109 1.8167 90.835 37.15158242 8.246889158 89.9 5.13 0.0039

Frozen

Tissue

2 Normal Fresh 109 1.81813 90.9065 57.28256516 8.616906774 92.13 4,49 0.0074

Frozen

Tissue

3 Normal Fresh 109 1.86759 93.3795 40.84166853 8.237797557 91.99 4.58 0.004

Frozen

Tissue Penalty

Starting Target 20x of

Tumor material Input Bases EXEX % Normal type Vol Cone DMA (ng) T^Jond Pico Catch Pico 20% data Adapter

Tumor Fresh 109 1.77499 88.7495 33.29778028 7.511627894 90.36 5,12 0.0058

Frozen

Tissue

Normal Fresh 109 1 .77296 88.648 40.20569617 8.34803994 93.22 4.42 0.0031

Frozen

Tissue

Tumor Fresh 109 1.53437 76.7185 37.88581392 8.5342048 92.45 5.42 0.0039

Frozen

Tissue

Nonnai Whole 109 2.33096 116,548 46,08534112 8.349775187 91,88 4,52 0.0055

Blood

Tumor Fresh 108 2.5^'W2 126,766 43,42787989 7.661691959 93 ,67 4.66 0.0041

Frozen

Tissue

Tumor Fresh 109 2.18836 109.418 45.47992022 8.462525076 93.1 4.43 0,0054

Frozen

Tissue

Tumor Fresh 109 2.05628 102.814 29.07540493 8.341633359 89.77 5,68 0.0328

Frozen

Tissue

Tumor Fresh 109 1 .76904 88.452 43.55318519 9.237733219 99 97 4.54 0.0053

Frozen

Tissue

Tumor Fresh 109 2.11737 105.8685 33.0199021 3 8.62361 3391 90.87 4.8 0.0346

Frozen

Tissue

Tumor Fresh 109 1.79304 89.552 29.81340002 8.470142363 90. 5,6 0.0083

Frozen

Tissue

Normal Fresh. 109 2.26163 1 13.0815 54.84925874 9.751777234 93.83 4.48 0.0088

Frozen

Tissue

Tumor Fresh 109 2.6033 130.165 69.24427699 8.694904985 90.53 4.97 0.0033

Frozen

Tissue

Tumor Fresh 109 2.41576 120,788 73,80338266 8.535117471 90, 18 5.2.1 0.0062

Frozen

Tissue

Normal Fresh 109 2.53819 126.9095 53.17976166 9.27343267 91.54 4.49 0.0141

Frozen

Tissue

Normal Whole 109 2.866 143.3 59.074993 8 9.849733782 91.31 4.53 0.0334

Blood

Normal ^"Whole 109 2.45236 122.618 61.99573961 9.923289052 90.6 4.63 0.003

Blood

Normal Whole 109 2.62712 131 ,356 54,02304075 9.632779063 93 .48 4.46 0.0072

Blood

Normal Fresh. 109 2.30707 1 15.3535 56.3659842 8.822538421 93.38 4.53 0.0076

Frozen

Tissue

Norma! ^"Whole 109 2.52406 126.203 72.34525108 9.59497345 91.35 4.57 0.0028

Blood

Normal Fresh 109 2.2751 8 113.759 61.42656935 8.281289809 91.56 4.48 0.0053

Frozen

Tissue

Tumor Fresh 54 2.40184 120,092 24,3 3097439 8.389406141 89.42 5.67 0.0189

Frozen

Tissue

Tumor Fresh 54 2.10047 105.0235 29.89457542 9.472640522 90.01 5.01 0,0043

Frozen

Tissue

Normal Fresh 54 2.0689 103.445 50.3195238 9.740017828 91.1 4.68 0.0083

Frozen

Tissue Penalty

Starting Target 20x of

Tumor materia! Input Bases EXEX % Normal type Vol Cone DNA (ng) T^Jond Pico Catch Pico 20% data Adapter

Normal Fresh 54 1.9048 95.24 38.83936659 10.27103645 90.35 4.88 0.0052

Frozen

Tissue

Normal Fresh 54 1 .7021 85.105 33.2339838 9.63 8948598 88.12 5.39 0.0125

Frozen

Tissue

Norma! Fresh 54 1.44885 72.4425 58.55141047 9.583249346 84.46 6.77 0.0026

Frozen

Tissue

Normal Fresh 54 1.23328 61.664 21 ,01247379 9.0117069 90,34 4.51 0.0086

Frozen

Tissue

Tumor Fresh. 54 0.63982 33.991 50.00286594 9.271186097 64.72 -3 0.0039

Frozen

Tissue

Norma! Fresh 105 2.70741 135.3705 17.49 11.08 94.01 4.28 0.0048

Frozen

Tissue

Normal Fresh 105 2.50468 125,234 24,99 11 ,81 93,5 4.51 0.0042

Frozen

Tissue

Normal Fresh 105 2.37286 1 38.643 43.67 12.29 90.57 4.54 0.0029

Frozen

Tissue

Norma! Whole 105 1.99647 99.8235 45.52 11.17 79.06 30.01 0.0032

Blood

Norma! Whole 105 1.82582 91.291 47.5 9.86 32.82 -1 0.001

Blood

Normal Fresh 105 3.21781 160.8905 53,05 13.5 93 .57 4.6 0.0032

Frozen

Tissue

Norma! Fresh 105 3.31762 165.881 50.84 11.74 91.67 4.57 0.0016

Frozen

Tissue

Norma! Fresh 105 3.04094 152.047 43.33 12.3 90.57 4.58 0.0018

Frozen

Tissue

Normal Fresh 105 2.78559 139.2795 43,26 12.16 90.89 4.54 0.005

Frozen

Tissue

Norma! Fresh 105 3.03596 151.798 9.54 8.95 93.89 5.11 0.0039

Frozen

Tissue

Tumor Fresh 105 2.74625 137.3125 9.91 12.71 88.14 4.8 0.0549

Frozen

Tissue

Normal Fresh. 109 2.55726 327.863 73 .6460049 7.664500812 89.61 8.37 0.3433

Frozen

Tissue

Norma! Fresh 109 2.97662 148.83 ! 80.40503965 8.577193439 80.2 6.68 0.2549

Frozen

Tissue

Norma! Fresh 109 2.68099 134,0495 70,16472956 7.068350846 90,37 0.2275

Frozen

Tissue

Tumor Fresh 109 1.64382 82.191 57.7673512 9.650875279 93.06 4.6 0.0056

Frozen

Tissue

Tumor Fresh 109 1.519! 5 75.9575 59.66844045 9.791205841 92.6 5.01 0.004

Frozen

Tissue

Normal Fresh 109 1 .69263 84.6315 65,79724232 8.034495566 92.87 4.45 0.0129

Frozen

Tissue Penalty

Starting Target 20x of

Tumor materia! Input Bases EXEX % Normal type Vol Cone DMA (ng) T^Jond Pico Catch Pico 20% data Adapter

79 Tumor Fresh 109 1.98945 99.4725 67.58262667 7.983114691 91.94 5.05 0.016

Frozen

Tissue

80 Tumor Fresh 109 1 .96723 98.3615 64.48375389 9.844428324 92.01 4.8 0.0029

Frozen

Tissue

81 Tumor Fresh 109 1.9! 651 95.8255 72.22055255 9.432828842 92.53 4.81 0.0023

Frozen

Tissue

82 Nonnai Fresh 109 1.80653 90.3265 64,05255617 9.114672571 93,08 4.41 0.0042

Frozen

Tissue

83 Tumor Fresh 109 1 .54006 77.003 55.6373572 9.538353004 92.6 4.74 0.0067

Frozen

issue

84 Norma! Fresh 109 2.00892 100.446 69.621821 1 8 7.86046357 92.39 4.57 0.01 54

Frozen

^'Tissue

85 Tumor Fresh 109 2.15865 107,9325 72,26077879 9.600378376 95,51 4.42 0.0072

Frozen

Tissue

86 Normal Fresh 109 1.72046 86.023 62.66275406 9.313713609 92.85 4.47 0.004

Frozen

Tissue

87 Normal Fresh 109 1.53125 76.5625 61.60539932 10.31757436 92.26 4.46 0.0053

Frozen

Tissue

88 ^'Tumor Fresh 109 1 .64316 82.1 58 53.92512797 8.920456546 93.06 4.61 0.0068

Frozen

Tissue

89 Tumor Fresh 109 1.86721 93.3605 65.42587569 9.971094152 92.79 4.54 0.0218

Frozen

Tissue

90 Tumor Fresh 109 1.92381 96.1905 59.17628619 9.727780847 92.32 4.77 0.0026

Frozen

Tissue

91 Tumor Fresh 109 1 .81177 90.5885 67.78426615 9.047048709 90.84 5.06 0.0021

Frozen

Tissue

92 Norma! Fresh 109 2.42249 121.1245 68.93478022 8.7113971 58 91.67 4.63 0.0027

Frozen

Tissue

93 Normal Fresh 109 1.89672 94.836 69,12556442 8.802998761 92,43 4.56 0.0081

Frozen

Tissue

94 Tumor Fresh 109 2.42152 123.076 73.88578163 9.01393659 95.65 4.43 0 ( H5

Frozen

Tissue

95 Tumor Cell Line, 109 1.981 13 99.0565 67.56447404 9.37577581 3 95.5 4.39 0.0097

Viable

96 Normal Fresh 109 2.08623 104.3115 68.26491 365 9.655147811 91.99 4.64 0.0029

Frozen

Tissue

97 Tumor Fresh 109 1 .7194 85.97 70.5722932 8.74778734 91.18 4.83 0.003

Frozen

Tissue

98 Tumor Fresh 109 1.72973 86.4865 60.5529821 9.100971004 92.84 4.56 0.0049

Frozen

Tissue

99 Tumor Fresh 109 1.50848 75,424 50,55207777 9.481852458 93, 17 4.83 0.0087

Frozen

Tissue Penalty

Starting Target 20x of

Tumor material Input Bases EXEX % Normal type Vol Cone DNA (ng) T^Jond Pico Catch Pico 20% data Adapter

100 Normal Fresh 109 1.98382 99.191 69.4531832 8.40042336 92.99 4.53 0.0042

Frozen

Tissue

01 Normal Fresh 109 1 .88544 94.272 65.3 8506282 9.361153442 92.59 4.46 0.005

Frozen

Tissue

102 Tumor FFPE 109 1.80382 90.091 36.67053923 8.402522593 90.49 5.21 0.0044

Embedded

Block

103 Tumor Fresh 109 2.05522 102,761 75,65728219 10,35087064 91, 13 4.76 0.0022

Frozen

Tissue

104 Tumor Fresh. 109 1 .77291 88.6455 65.460402 9.079424185 92.97 4.47 0.0031

Frozen

Tissue

105 Norma! Fresh 109 2.08954 104.477 76.69234549 8.332543473 92.03 4.52 0.002

Frozen

Tissue

106 Tumor FFPE 109 1.94523 97.2615 62,36185596 8.449299447 91,8 4.79 0.0026 iimbedded

Block

107 Tumor Fresh 109 1.85839 92.9195 58.7707563 7.797480562 95.5 4.39 0.0049

Frozen

Tissue

108 Normal Whole 109 2.20394 110.197 63.32997234 8.402227936 94.92 4.46 0.0036

Blood

109 Tumor Cell Line, 109 1.81383 90.6915 67.95562704 8.906312994 95.65 4.41 0.005

Viable

110 Tumor Fresh 109 1 .62325 81.1625 55.21287596 9.566234956 92.19 4.55 0.0047

Frozen

Tissue

111 Tumor Fresh 109 1.99324 99.662 67.71699248 7.940094718 92.54 4,64 0.0038

Frozen

Tissue

112 Tumor Fresh 109 2.17047 108.5235 75.10398985 7.427796087 90.85 5.01 0.0018

Frozen

Tissue

113 Normal Whole 109 1 .9964 99.82 68.79950678 7.378842452 90.99 4.6 0.0042

Blood

114 Normal Whole 109 1.95507 97.7535 65.07792597 9.777393778 92.12 4.5 0.0043

Blood

115 Tumor Cell Line. 109 1. 1766 90.883 60.7768404 10.26317325 95.51 4,42 0.0243

Viable

1 16 Tumor Fresh 109 1.65276 82.638 64.178973 3 3 9.515185571 92.68 4.51 0.0022

Frozen

Tissue

117 Tumor Fresh 109 1.82637 91.3185 64,75161418 7.512988892 91,88 4.62 0.0032

Frozen

Tissue

118 Normal Fresh 109 1.62824 83.412 53.89330343 7.485806752 93.14 4.45 0.0048

Frozen

Tissue

1 19 Normal Fresh 109 1.88856 94.428 73.39982039 9Λ? 5?77585 92.42 4.55 0.0033

Frozen

Tissue

120 Tumor Fresh 109 1 .64159 82.0795 63.26084711 8.320681515 92.62 4.46 0.0047

Frozen

Tissue

121 Normal Fresh 109 1.66907 83.4535 55.4817528 8.055526734 93.09 4,52 0.0087

Frozen

Tissue

122 Normal Fresh 109 1.74835 87.4175 54.48608072 9.788259268 92 4.61 0.0097

Frozen

Tissue Penalty

Starting Target 20x of

Tumor materia! Input Bases EXEX % Normal type Vol Cone DNA (ng) Pond Pico Catch Pico 20% data Adapter

123 Normal Fresh 109 1.91207 95.6035 60.5027356 9.892052318 92.14 4.54 0.0056

Frozen

Tissue

124 Normal Fresh 109 2.1027 105.1 35 68.29566221 9.057877367 93.88 4.56 0.0024

Frozen

Tissue

1 5 Norma! Fresh 109 1.96449 98.2245 70.92129578 8.7614! 5243 93.06 4.48 0.0028

Frozen

Tissue

126 Nonnai Fresh 109 2.3713 118,565 75,49281931 9.224506097 92,2 4.52 0.0032

Frozen

Tissue

127 Normal Fresh 109 ~> T59 4 1 3 3 .492 63.99297922 9.375407491 92.35 4.48 0.0039

Frozen

Tissue

1 8 Norma! Whole 109 2.48369 124.1845 78.19030301 8.939277784 87.05 7.44 0.0023

Blood

129 Tumor Fresh 109 2.01 389 100.5945 60.8861 3927 10.30077889 90.63 5.21 0.0222

Frozen

Tissue

130 Tumor Fresh. 109 2.14403 307.2015 72.64285547 8.986680785 93.07 4.95 0.001

Frozen

Tissue

1 31 Norma! Ce!! Line, 109 1.88377 94.1885 63.75989937 7.33948728 10.52 -1 0.023 3

Viable

1 32 Tumor Fresh 109 1.69927 84.9635 57.44746545 8.569853 335 93.06 4.67 0.0039

Frozen

Tissue

133 Tumor Fresh 54 1 .90439 95.2395 62.78847921 1.80071735 2.6 -3 0.2883

Frozen

Tissue

134 Norma! Fresh 54 2.26875 113.4375 77.34003155 3.942581611 0.08 -1 0.1465

Frozen

Tissue

135 Tumor Fresh 54 2.05803 102.9015 61.33803099 2.439939634 0.7 -1 0.2066

Frozen

Tissue

136 Tumor Fresh 54 2.03655 103 .8275 67.03764824 6.084316959 0.27 -3 0.1013

Frozen

Tissue

137 Tumor Fresh 54 2.13458 106.729 60.73164034 10.16472086 91.64 4,88 0.0018

Frozen

Tissue

138 Tumor FFPE 54 2.61324 130.662 17.57520059 7.393137016 94.87 4.59 0.0034

Embedded

Block

139 Normal Whole 109 3.01496 350.748 74.2359308 8.963292358 94.28 5.59 0.0037

Blood

140 Norma! Whole 109 2.72355 136.1775 67.52646242 8.908449259 95.55 4,54 0.0015

B!ood

141 Norma! Whole 109 2.60505 130.2525 65.1644053 2 10.39193851 95.6 4.32 0.0256

Blood

142 Tumor FFPE 109 1.23796 61.898 5.350750842 6.73310824 85.09 8.07 0.3952

Embedded

Block

143 Tumor FFPE 109 0.91743 45.8715 6.068930839 7.636229461 87.94 6.52 0.1341

Embedded

Block

144 Tumor FFPE 54 2.61324 130.662 16.61942801 8.393314551 94.87 4,59 0.0032

Embedded

Block

145 Normal Whole 109 3.01496 150.748 68.71513332 9.625718908 94.28 5.59 0.0041

Blood Penalty

Starting Target 20x of

Tumor material Input Bases EXEX % Normal type Vol Cone DMA (ng) Pond Pico Catch Pico 20% data Adapter

146 Normal Whole 109 2.72355 136.1775 68.19008648 8.681342309 95.55 4.54 0.002

Blood

147 Nonnai Whole 109 2.60505 130,2525 74,07655066 9.514817249 95,6 4.32 0.0049

Blood

148 Tumor FFPE 109 1 .23796 61.898 4.72529814 7.796670254 85,09 8.07 0.1857

Embedded

Block

149 Tumor FFPE 109 0.91743 45.8715 7.875738936 8.024919202 87.94 6.52 0.1296

Embedded

Block

150 Normal Whole 109 3.82696 191.348 14.21 12.72463387 NA NA 0.1499

Blood

151 Tumor Fresh 109 3.5284S 176,424 83,91 12,06646181 NA NA 0.0081

Frozen

Tissue

152 Normal Whole 109 4.02543 203.2715 79.22 12.6802603 NA NA 0.0126

Blood

1 53 Norma! ^•Whole 109 3.88267 194.1335 71.74 12.57045086 NA N 0.0738

Blood

1 54 Normal Whole 109 3.89542 194.771 78.65 12.86063385 NA NA 0.0097

Blood

155 Normal Whole 109 3.82682 191.341 80.82 12.79264348 NA NA 0.006

Blood

156 Tumor Fresh 109 3.68127 184,0635 64,59 13,2815172 NA NA 0.0329

Frozen

Tissue

157 Tumor Fresh 109 3.80863 190.4315 72.61 12.53212148 NA NA 0.0096

Frozen

Tissue

1 58 Normal Whole 109 3.89365 194.6825 83.3 12.31845633 NA NA 0.0036

Blood

159 Normal Whole 109 3.80826 190.413 82.2 12.28675005 NA NA 0.0044

Biood

160 Normal Whole 109 3.72574 186.287 76.48 12.7568486 NA NA 0.0133

Blood

161 Normal Whole- 109 3.9236 196.3 8 83.52 13.49257539 NA NA 0.0045

Blood

162 Normal Whole 109 3.99427 199.7135 86.1 13.10998618 NA NA 0.0037

Blood

163 Tumor Fresh 109 3.87775 193.8875 74.38 13.8289791 NA NA 0.0077

Frozen

Tissue

164 Normal Whole 109 3.83966 191.983 77.21 12.06519355 NA NA 0.0041

Biood

165 Normal Whole 109 3.63936 181 .968 75.36 13.22381176 NA NA 0.01

Blood

166 Normal Whole- 109 3.54378 177.3 89 66.22 12.25366982 NA NA 0.0144

Blood

167 Normal Whole 109 3.89928 194.964 69.59 13.29212119 NA NA 0.0065

Blood

168 Normal Whole 109 3.84211 192.1055 87.2 13.63035682 NA NA 0.0085

Blood

169 Normal Whole 109 3.7266 186.33 74.69 12.77449843 NA NA 0.03 22

Blood

170 Tumor Fresh 109 4.0434 202.07 71.34 13.66449392 NA NA 0.0083

Frozen

Tissue

171 Normal Whole- 109 3.80572 190.286 90.21 12.73588722 NA NA 0.0272

Blood

172 Tumor Fresh 109 3.67088 183.544 68 12.3845111 NA NA 0.0071

Frozen

Tissue

1 73 Normal Whole 109 3.96652 198.326 74.85 13.2884223 2 NA NA 0.03 39

Blood Penalty

Starting Target 20x of

Tumor materia! Input Bases EXEX % Normal type Vol Cone DMA (ng) T^Jond Pico Catch Pico 20% data Adapter

174 Normal Whole 109 3.90082 195.04! 65.51 13.7540838 NA NA 0.0284

Blood

175 Nonnai Whole 109 3.96616 198,308 78,44 12,6264653 NA NA 0.0081

Blood

176 Tumor Fresh 109 3.74302 187,1 51 76,99 12.30X33494 NA NA 0.007

Frozen

Tissue

177 Tumor Fresh 109 3.93065 196.5325 69.37 13.19689664 NA NA 0.0752

Frozen

Tissue

178 Normal ^"Whole 109 3.82937 191.4585 79.38 12.17577804 NA NA 0.0064

Biood

179 Tumor Fresh 109 3.87818 193,909 79,21 13,28215132 NA NA 0.0095

Frozen

Tissue

180 Normal ^"Whole 109 3.865 193.25 74.84 12.8772268 NA NA 0.0172

Blood

1 81 Norma! ^"Whole 109 3.96056 198.028 72.14 12.42456671 NA N 0.01 17

Blood

1 82 Normal Whole 109 3.92625 196.3125 65.43 13.73773545 NA NA 0.01 87

Blood

1 83 Tumor Fresh 109 4.00871 200.4355 77.74 13.6883441 NA NA 0.0172

Frozen

Tissue

184 Normal ^"Whole 109 3.69825 184.9125 76.07 12.1 2747879 NA NA 0.0056

Blood

185 Normal ^"Whole 109 4.02197 201.0985 78.34 12.57971614 NA NA 0.0065

Blood

1 86 Norma! ^"Whole 109 3.90294 195.147 84.04 11.69581531 NA N 0.0039

Blood

1 87 Norma! Whole 109 3.5721 2 178.606 73.76 12.4585981 2 NA NA 0.0065

Blood

1 88 Norma! ^"Whole 109 3.83883 191.9415 79.67 13.2616831 5 NA NA 0.0085

Biood

189 Tumor Fresh 109 3.6495 182,475 68,88 12,4431325 NA NA 0.0114

Frozen

Tissue

190 Tumor Fresh 109 3.94992 197.496 57.37 12.96293947 NA NA 0.0115

Frozen

Tissue

191 Norma! Whole 108.58603 3.972 198.6 57.81 13.34017383 NA NA 0.009

Blood

192 Norma! ^"Whole 109 3.84484 192.242 81.13 11.67245834 NA NA 0.004

Biood

193 Normal Whole 109 3.87934 193,967 73,1 Ϊ 1 ,69292651 NA NA 0.0084

Blood

194 Normal ^"Whole 109 3.78521 189.2605 72.1 1 12.2074491 NA NA 0.009

Blood

195 Normal ^"Whole 109 3.63003 183.5015 75.06 12.04853014 NA NA 0.0093

Blood

196 Norma! Whole 109 3. 1 63 190.9315 39.83 11.79805047 NA NA 0.013

Blood

197 Tumor Fresh 109 3.67427 183.7135 65.31 12.84330108 NA NA 0.01 59

Frozen

Tissue

198 Tumor Fresh 109 3.59435 179.7175 73,47 12.64140248 NA NA 0.1431

Frozen

Tissue

199 Norma! Whole 109 3.97947 198.9735 78.37 12.80028621 NA NA 0.0029

Blood

200 Tumor Fresh 109 3.64523 182.2615 67.18 12.70069324 NA N 0.0077

Frozen

Tissue Penalty

Starting Target 20x of

Tumor materia! Input Bases EXEX % Normal type Vol Cone DNA (ng) Pond Pico Catch Pico 20% data Adapter

201 Normal Whole 109 3.78534 189.257 57.28 13.19788306 NA NA 0.0288

Blood

202 Tumor Fresh 109 3.87297 193,6485 68,9 13,73724224 NA NA 0.0094

Frozen

Tissue

203 Normal Whole 109 3.7 W9 186.6695 60.44 13.97778727 NA NA 0.0116

B!ood

204 Normal Whole 109 3.87273 193.6365 64.1 14.13068203 NA NA 0.0234

Blood

205 Norma! ^'Whole 109 3.72446 186.223 70.22 13.57208771 NA N 0.0101

Blood

206 Normal ^"Whole 109 3.75589 187.7945 70.82 13.01937666 NA NA 0.0069

Blood

207 Normal Whole 109 3.75429 187,7145 75,68 13,50768872 NA NA 0.0099

Blood

208 Normal Whole 109 3.90926 ! 95, 463 70,95 13.65149434 NA NA 0.0134

Blood

209 Normal Whole- 109 3.88342 194.1 71 77.63 12.95719711 NA NA 0.0114

Blood

210 Normal Whole 109 3.73678 186.839 56.77 14.18648 1 NA NA 0.0163

B!ood

21 i Tumor Fresh 109 3.937! 196.855 86.82 13.8964078 NA N 0.0125

Frozen

Tissue

212 Tumor Fresh 109 3.7958 189,79 61 ,05 13,60936021 NA NA 0.196

Frozen

Tissue

213 Normal Whole 109 3.85869 192.9345 74.87 13.53079908 NA NA 0.003

B!ood

214 Tumor Fresh 109 3.86201 193.1005 67.87 14.03834628 NA NA 0.0098

Frozen

Tissue

215 Normal Whole 109 3.92634 196.307 66.1 12.72052729 NA NA 0.0071

Blood

216 Tumor Fresh 109 3.72623 186,3115 63,83 13,76482671 NA NA 0.0081

Frozen

Tissue

217 Normal Whole 109 4.03458 203.729 77.83 13.93519516 NA NA 0.0092

B!ood

218 Normal Whole 109 3.97073 198.5365 61.83 14.62339774 NA NA 0.1228

Blood

219 Normal Whole 109 3.8465 192.325 67.12 14.243521 19 NA NA 0.1099

Blood

220 Normal Whole 109 3.68409 184.2045 56.43 13.22828587 NA NA 0.01 18

Blood

221 Normal Whole 109 3.69442 184,721 77,83 14,42829839 NA NA 0.0441

Blood

222 Normal Whole- 109 3.95896 197.948 69.56 13.78332204 NA NA 0.007

Blood

223 Normal Whole 109 3.98432 199.216 60.77 13.48461358 NA NA 0.0061

Blood

224 Normal Whole 109 3.67152 183.576 63.35 14.66831498 NA NA 0.0052

Blood

225 Norma! Fresh 109 3.87 193.5 52.41 15.18724122 NA N 0.4076

Frozen

Tissue

226 Tumor Fresh 109 3.48453 174,2265 65,29 14,63879291 NA NA 0.2097

Frozen

Tissue

227 Normal Fresh 109 3.66969 183.4845 65.49 1 3.332884 NA NA 0.0234

Frozen

Tissue

228 Norma! Whole 109 3.79256 189.628 64.14 14.16242355 NA NA 0.0344

Blood Penalty

Starting Target 20x of

Tumor material Input Bases EXEX % Normal type Vol Cone DNA (ng) Pond Pico Catch Pico 20% data Adapter

229 Normal Whole 109 3.77021 188.5105 64.98 13.62214841 NA NA 0.0328

Blood

230 Nonnai Whole 109 3.7789S 188,949 70,22 13,6507193 NA NA 0.0338

Blood

23 ϊ Normal Whole 109 4.04717 202.3585 73 ,3 1 15,31318564 NA NA 0.0245

Blood

232 Tumor Fresh 109 2.39483 1 39.7415 57.23 14.64682516 NA NA 0.0258

Frozen

Tissue

233 Tumor Fresh 109 4.04512 202.256 66.96 14.08657507 NA N 0.2757

Frozen

^'Tissue

234 Normal Whole 109 2.51877 125,9385 62,35 12,21030266 NA NA 0.0898

Blood

235 Unknown FFPE 109 2.39901 1 39.9505 35.99328356 30.63893378 82.53 5.46 0.0288

Tissue

Section

236 Unknown FFPE 109 1.58509 79.2545 30.11158281 10.91467472 82.73 5.01 0.0068

Tissue

Section

237 Tumor Fresh 109 2.01114 100,557 78,6174582 13,18430311 79,93 4.93 0.0074

Frozen

Tissue

238 Tumor Fresh 109 1 .90021 95.0305 80.8502722 32.59708848 83.22 4.63 0.0166

Frozen

Tissue

239 Tumor Fresh 109 1.87737 93.8685 80.8908337 12.41320968 81.68 4.75 0.0053

Frozen

^'Tissue

240 Unknown FFPE 109 2.54718 127,359 30,36692711 12,34919977 82,99 4.74 0.0053

Tissue

Section

241 Tumor Fresh 109 2.10008 105.004 73.46502743 13.78770371 81.82 4.8 0.0194

Frozen

Tissue

242 Normal Whole 109 2.23524 111.762 72.84068937 12.8004368 82.13 4.53 0.0072

Blood

243 Unknown FFPE 109 2.31 3 115.55 33.24822292 12.9375733 82.63 5.24 0.0025

^'Tissue

Section

244 Tumor Fresh 109 2.07605 303.8025 67.03147134 32.69992154 79.61 5.02 0.0027

Frozen

Tissue

245 Tumor Fresh 109 2.09512 104.756 70.27310779 14.54620376 81.75 4.91 0.0053

Frozen

^'Tissue

246 Tumor Fresh 109 1.87233 93.6165 74,36116617 13,60297505 81,87 4.76 0.0033

Frozen

Tissue

247 Tumor Fresh 109 1.95493 97.7465 72.85251015 13.56368834 80.76 4.96 0.0016

Frozen

Tissue

248 Normal Whole 109 2.03484 101.742 40.4027307 14.4093763 79.4 4.6 0.0066

Blood

249 Tumor Fresh 109 1.95444 97.722 72.64962539 13.96845348 79.5 5.02 0.0571

Frozen

Tissue

250 Tumor FFPE 109 1 .92085 96.0425 64.23809741 33.09201604 73.39 6.36 0.002

Embedded

Block

25 i Unknown FFPE 109 2.02178 101.089 16.43424501 12.08242099 80.75 5.62 0.0038

Tissue

Section Penalty

Starting Target 20x of

Tumor material Input Bases EXEX % Normal type Vol Cone DNA (ng) Pond Pico Catch Pico 20% data Adapter

252 Tumor FFPE 109 2.02363 101.0815 44.86963349 13.39190073 81.54 5.53 0.0347

Embedded

Block

253 Tumor Fresh 1 .95692 97.846 76.03589256 32.3 3974791 83.52. 4.75 0.0046

Frozen

Tissue

254 Unknown FFPF. 5■ 1.16402 58.201 6.893693472 9.62628696 65.63 -1 0.0336

Tissue

Section

255 Unknown FFPE 51 0.92193 46.0965 32,25122125 13,75336164 81,26 4.96 0.0134

Tissue

Section

256 Unknown FFPE 1 .19641 59.8205 27.92732672 32.82987286 82.52. 5.33 0.0168

Tissue

Section

257 Tumor Fresh 5■ 0.69376 34.688 46.75933583 12.43750795 80.72 4.7 0.0203

Frozen

Tissue

258 Unknown FFPE 51 1.2648 63.24 48,30940321 12,84586568 81,03 4.71 0.0201

Tissue

Section

259 Tumor Fresh 2.68944 134.472 83.6922813 12.18973513 80.35 4.68 0.0014

Frozen

Tissue

260 Unknown FFPE 51 0.84509 42.2545 19.9033349 9.30106099 82.47 4.99 0.0052

Tissue

Section

26 ϊ Tumor FFPE 50 i .84966 92.483 34,77719832 10,25464254 84,04 4.75 0.0156

Tissue

Section

262 Normal Whole 109 2.16654 108.327 53.92695 7.938788588 89.07 5.14 0.2278

Biood

263 Tumor Fresh 109 1.79034 89.517 50.603475 8.13107723 2 91.94 4.58 0.0368

Frozen

Tissue

264 Tumor Fresh 109 2.23506 111 ,753 51 ,73815 8.358604413 92,57 4.33 0.025

Frozen

Tissue

265 Normal Whole 109 2.02242 103.121 56.4 8.802438392 93.2 5.1 0.0566

Blood

266 Normal Whole 109 2.08929 104.4645 61.0762125 7.625190361 91.98 4.5 0.0045

Biood

267 Tumor Fresh 109 2.51 381 125.5905 60.816375 8.584984477 91.72 4.64 0.0068

Frozen

Tissue

268 Normal Whole 109 2.2512 1 32.56 54,9616875 8.783116324 93, 19 4.4 0.1721

Blood

269 Tumor Fresh 109 2.6079 330.395 68.39 34.3401 95.02. 4.52 0.0033

Frozen

Tissue

270 Tumor FFPE 109 2.51 303 125.5515 54.37 15.5489 89.48 5.37 0.0032

Tissue

Section

27Ϊ Normal Whole 109 2.21808 110,904 78,53 14,83885 89,23 4.41 0.0014

Blood

272 Tumor Fresh 109 2.39184 1 39,592 64,26 14,76665 89,22 4.63 0.003

Frozen

Tissue

273 Normal Whole 109 2.39132 119.566 69.78 15.71345 86.9 4.48 0.0027

Biood

274 Tumor Fresh 109 2.21406 110.703 65.43 17.21055 88.81 4.48 0.0033

Frozen

Tissue Penalty

Starting Target 20x of

Tumor material Input Bases EXEX % Normal type Vol Cone DMA (ng) T^Jond Pico Catch Pico 20% data Adapter

275 Normal Whole 109 2.16935 108.4675 70.12 15.3722 88.1 4.51 0.0024

Blood

276 Normal Whole 109 2.25202 112,601 76,1 17,03855 89,23 4.41 0.0019

Blood

277 Tumor Fresh 109 2.79676 139.838 81 ,3 Ϊ 6,4459 94,79 5.25 0.0014

Frozen

Tissue

278 Tumor Fresh 109 2.65334 132.667 75.34 17.444 95.4 4.66 0.0018

Frozen

Tissue

279 Normal ^"Whole 109 3.15326 157.563 72.76 17.12975 89.04 4.67 0.0018

Blood

280 Normal Whole 109 3.02516 151 ,258 83,36 17,5049 89,04 4.67 8.00E- Blood 04

28 S Tumor Fresh 54 0.47 23.5 35.3 17.417 95.33 5.03 0.0055

Frozen

Tissue

282 Norma! Fresh 105 1.49723 74.8615 5.24 14.1793 57.29 -1 0.1837

Frozen

Tissue

283 Normal Fresh 105 1.56839 78.4195 5.21 13,10925 60,35 -1 0.0933

Frozen

Tissue

284 Normal Fresh 105 2.94667 147.3335 47.87 15.6736 93.5 4.53 0.0016

Frozen

Tissue

285 Norma! Fresh 105 2.96944 148.472 42.14 16.09405 94.01 4.28 0.0036

Frozen

^'Tissue

286 Normal Fresh 105 1.84412 92.206 20,73 14,8694 81,53 6.69 0.0134

Frozen

Tissue

287 Normal Fresh 105 3.05505 152.7525 8.61 14.5343 79.99 8.89 0.017

Frozen

Tissue

288 Norma! Fresh 105 2.08054 104.027 7.41 15.2585 75.87 -1 0.03 85

Frozen

^'Tissue

289 Normal Fresh 105 0.98186 49.093 4.97 13.7169 64.14 -3 0.1346

Frozen

Tissue

290 Norma! Fresh 105 1.39808 69.904 12.79 16.3019 84.13 8.6 0.0506

Frozen

Tissue

291 Norma! Fresh 105 0.78771 39.3855 7.86 13.6323 78.26 10.45 0.1352

Frozen

Tissue

292 Normal Fresh 105 0.9776 48.88 6.65 14.3679 73.26 -1 0.0295

Frozen

Tissue

293 Norma! Fresh 105 1.5073 75.365 10.21 13.7814 85.95 5.38 0.0132

Frozen

Tissue

294 Norma! Fresh 105 2.85528 142,764 15,69 15,50305 93,89 5.11 0.0037

Frozen

Tissue

295 Norma! Fresh 105 2.83321 143.6605 3.41 12.3418 67.87 -1 0.0665

Frozen

Tissue

296 Norma! Fresh 109 2.55726 127.863 71.6460049 7.6645008 J 2 NA NA 0.3433

Frozen

^'Tissue Penalty

Starting Target 20x of

Tumor materia! Input Bases EXEX % Normal type Vol Cone DNA (ng) T^Jond Pico Catch Pico 20% data Adapter

297 Normal Fresh 109 2.97662 148.83 ! 80.40501965 8.577193439 NA NA 0.2549

Frozen

Tissue

298 Normal Fresh 109 2.68099 134.0495 70.16472956 7.068350846 NA NA 0.2275

Frozen

Tissue

299 Norma! Fresh 109 2.25949 112.9745 51.08 8.22 90.4 4.63 0.0548

Frozen

Tissue

300 Tumor Fresh 109 2.52777 126,3885 56,95 12,61 90,78 4,68 0.0703

Frozen

Tissue

30 S Normal Whole 109 2.85896 142.948 70.04 13.96 91.47 4.6 0.0217

Blood

302 Normal Whole 109 2.32521 116.2605 53.85 13.68 91.1 4.56 0,0619

B!ood

303 Norma! Whole 109 2.96226 148.113 68.94 12.71 91.9 4.55 0.0426

Blood

304 Norma! Whole 109 3.27437 163.7185 62.94 15.25 91.12 4.56 0.0526

Blood

305 Tumor Fresh 109 2.513 125,65 48,73 15,19 90,68 4,79 0.0995

Frozen

Tissue

306 Normal Fresh. 109 2.59082 129.541 59.38 14.71 90.2 4.64 0.039

Frozen

Tissue

307 Tumor Fresh 109 2.37649 118.8245 57.37 16.76 90.42 4.77 0.0325

Frozen

^'Tissue

308 Normal Fresh 109 2.3578 117,89 60,1 16,5 91,09 4,61 0.0374

Frozen

Tissue

309 Normal Whole 109 2.69837 134.9185 76.06 18.26 91.17 4.56 0,0246

B!ood

310 Norma! Whole 109 2.72924 136.462 76.73 16.86 91.19 4.72 0,0206

Blood

311 Norma! Whole 109 2.68552 134.276 69.09 17.23 90.69 4.55 0.0238

Blood

312 Norma! Fresh 109 2.52335 126.1675 54.2 18.04 91.01 4,6 0.0578

Frozen

Tissue

313 Normal Fresh 109 2.51205 125.6025 56.6 17.22 90.8 4.71 0.1098

Frozen

Tissue

314 Tumor Fresh 109 2.52229 126.1145 52.42 15.13 89.81 4.83 0.031 1

Frozen

Tissue

315 Normal Fresh 109 2.25605 112,8025 55,14 16,73 90, 16 4,78 0.0343

Frozen

Tissue

316 Tumor Fresh 109 2.36468 1 38.234 67.64 16.67 91.55 4.65 0,0245

Frozen

Tissue

317 Norma! Whole 109 2.8885 144.425 68.48 16.79 91.38 4.55 0.014

Blood

318 Norma! Whole 109 2.81072 140.536 77.18 16.8 90.61 4,64 0.0185

Blood

319 Normal Whole 109 2.43585 121 ,7925 67,81 17,95 90,97 4,58 0.027

Blood

320 Normal Whole 109 2.83714 141 ,857 69,83 18.1 7 91 ,65 4.68 0.0306

Blood

321 Normal Whole 109 1.77211 88.6055 73.67 15.11 88.78 4.95 0,0674

Blood Penalty

Starting Target 20x of

Tumor materia! Input Bases EXEX % Normal type Vol Cone DMA (ng) Pond Pico Catch Pico 20% data Adapter

322 Normal Fresh 109 2.39267 119.6335 64.6 15.31 90.55 4,53 0.3382

Frozen

Tissue

323 Tumor Fresh 109 2.59088 129.544 56.4 16.83 90.51 4.82. 0.0281

Frozen

Tissue

324 Norma! Fresh 109 2.33722 116.86! 53.39 16.07 90.87 4.56 0.0268

Frozen

Tissue

325 Normal Whole 109 2.24951 112,4755 74,35 17,18 91,67 4.66 0.0132

Blood

326 Normal Whole 109 2.43618 123 .809 60,03 17.] J. 89,61 4.73 0.0277

Blood

327 Normal Whole 109 2.451 12.2.55 68.4 17.07 91.05 4.57 0.0442

Blood

328 Normal Fresh 109 2.49709 124.8545 58.54 17.52 91.23 4.53 0.062

Frozen

Tissue

32.9 Tumor Fresh 109 2.46588 123.294 60.9 16.79 90.39 4.75 0.0562

Frozen

Tissue

330 Tumor Fresh 109 2.57971 128,9855 68,94 13 3^'? 89,88 4.82 0.0411

Frozen

Tissue

331 Normal Fresh 109 2.28843 114.4215 65.02 15.92 90.4 4.72 0.0602

Frozen

Tissue

332 Normal Whole 109 2.6133 130.665 74.17 16.29 90.36 4.74 0.0344

Blood

333 Normal Whole 109 2.36094 118,047 78,51 17,2 91,29 4.64 0.0237

Blood

334 Normal Whole 109 2.63548 131 .774 79.87 17.38 90.2 4.79 0.0195

Blood

335 Normal Whole 109 2.77279 138.6395 64.77 18.35 91.04 4.62 0.0485

Blood

336 Normal Whole 109 2.65032 132.516 57.7 17.68 91.29 4.6 0.0358

Blood

337 Norma! ^'Whole 109 2.6527 132.635 57.59 16.39 90.6 4.76 0.0274

Blood

338 Tumor Fresh 109 2.56692 128.346 64 16.69 89.73 4.97 0.0309

Frozen

Tissue

339 Tumor Fresh 109 2.3823 Ϊ 19,1 15 59,44 16.] 5 90,32 4.85 0.0288

Frozen

Tissue

340 Norma! Whole 109 2.78244 139.122 69.19 15.73 91.07 4.74 0.0224

Blood

341 Norma! Whole 109 1.962.35 98.1175 80.8! 16.56 87.03 7.17 0.0348

Blood

342 Norma! Whole 109 2.29544 114.772 54.8 16.55 90.35 4.71 0.0573

Blood

343 Norma! Whole 109 2.73396 136,698 47,15 16,77 91,77 4.59 0.0252

Blood

344 Normal Whole 109 3.06872 Ϊ 53 ,436 72,51 17.66 91 ,02 4.61 0.0198

Blood

345 Norma! Fresh 109 2.55324 127.662 55.96 14.62 90.72 4.74 0.0653

Frozen

Tissue

346 Norma! Fresh 109 2.34017 117.0085 60.26 15.6 89.97 4.65 0.0362

Frozen

Tissue

347 Normal Fresh 109 2.40796 120.398 52,19 15.36 91 ,5 4.77 0.0762

Frozen

Tissue Penalty

Starting Target 20x of

Tumor material Input Bases EXEX % Normal type Vol Cone DMA (ng) r^jond Pico Catch Pico 20% data Adapter

348 Normal Whole 109 2.84395 142.1975 73.17 16.13 90.49 4.88 0.0237

Blood

349 Normal Whole 109 2.53117 126,5585 80,05 16,88 90,92 4.68 0.0159

Blood

350 Normal Whole 109 2.58944 129.472 55,39 15,63 90,23 4.76 0.0263

Blood

351 Normal Whole 109 2.82395 143.1975 58.26 17.53 91.73 4.63 0.0492

Blood

352 Tumor Fresh 109 2.80701 140.3505 48.63 16.56 90.97 4.84 0.0597

Frozen

Tissue

353 Normal Whole 109 2.85054 142.527 66.25 10.32 90.02 4.86 0.0793

Blood

354 Normal Fresh 109 2.59949 129,9745 62,96 14,71 90,39 4.6 0.027

Frozen

Tissue

355 Tumor Fresh 109 2.59852 129.926 53.94 15.6 90.95 4.77 0.0525

Frozen

Tissue

356 Normal Whole 109 2.21595 110.7975 69.83 16.86 89.63 5.16 0.0073

Blood

357 Normal Whole 109 2.843 3 1 142.0555 81.32 17.6 90.89 4.82 0.0222

Biood

358 Normal Whole 109 3.02696 151 ,348 61 ,49 16,43 91,29 4.73 0.0395

Blood

359 Normal Whole- 109 2.44586 122.293 53 .94 18.25 90.73 4.6 0.0607

Blood

360 Normal Whole 109 2.95687 147.8435 70.11 18.04 91.24 4.74 0.0292

Blood

361 Normal Whole 109 2.89043 144.5215 65.3 16.96 90.21 4.79 0.0428

Blood

362 Tumor Fresh 109 2.49856 124.928 58.28 15.39 89.52 4.71 0.0599

Frozen

Tissue

363 Tumor Fresh 109 2.83863 141 ,9315 68,91 17,04 90,09 4.91 0.0406

Frozen

Tissue

364 Normal Whole 109 2.69516 134.758 73.45 16.89 90.93 4.67 0.0404

Blood

365 Normal Whole 109 3.24868 162.434 78.85 17.01 89.9 4.85 0.0298

Blood

366 Normal Whole 109 2.50337 125.1685 55.68 16.47 91.16 4.71 0.0375

Blood

367 Normal Whole 109 2.43275 121.6375 59.56 18.1 90.75 4.7 0.0531

Biood

368 Tumor Fresh 105 2.80278 140,139 29,25 11 ,39 88,3 4.59 0.0034

Frozen

Tissue

369 Tumor Fresh 105 2.74868 137.434 39.07 12.43 88.25 4.62 0.0035

Frozen

Tissue

370 Normal Whole 105 2.77244 138.622 74.19 13.25 86.94 4.5 0.0017

Blood

371 Normal Whole 105 2.22335 111.1575 66.42 12.57 87.51 4.54 0.0033

Biood

372 Normal Whole 105 2.71104 135.552 49.46 9.8) 89.36 4.43 0.0052

Blood

373 Normal Whole- 105 2.65216 132.608 72.62 13.1 5 85.37 4.44 0.0038

Blood

374 Normal Whole 105 2.22001 1 3 3.0005 43.21 13.5 87.34 4.39 0.0147

Blood

375 Tumor Fresh 105 2.69668 134.834 26.93 12.56 86.28 5.23 0.0056

Frozen

Tissue Penalty

Starting Target 20x of

Tumor material Input Bases EXEX % Normal type Vol Cone DMA (ng) Pond Pico Catch Pico 20% data Adapter

376 Normal Whole 105 2.34638 117.309 51.29 13.15 87.99 4.56 0.0036

Blood

377 Tumor Fresh 105 2.17014 108,507 43,55 10,93 88,49 4.5 0.0032

Frozen

Tissue

378 Normal Whole 105 2.98878 349.439 73.23 33.77 86.18 4.52 0.0042

B!ood

379 Normal Whole 105 2.83118 141.559 52.41 11.86 88.69 4.46 0.0017

Blood

380 Norma! ^'Whole 105 2.90201 145.1005 63.11 13.58 86.27 4.53 0.0023

Blood

381 Normal ^"Whole 105 2.65398 132.699 79.25 13.56 87.52 4.71 0.0015

Blood

382 Normal Whole 105 2.9883 149, 15 67,97 5.46 0 -1 1.2235

Blood

383 Normal Whole 105 2.08242 !04,1 i 47,06 13.75 86,71 4.45 0.0033

Blood

384 Normal Whole- 105 2.82425 343 .2125 63 .39 32.94 88.45 4.36 0.0032

Blood

383 Normal Whole 105 2.33205 116.6025 50.84 12.59 88.98 4.57 0.0045

B!ood

386 Norma! ^"Whole 105 2.79663 139.8315 59.99 10.74 88.96 4.42 0.0022

Blood

387 Norma! Whole 105 2.7591 137.955 66.26 12.51 88.22 4.42 0.0036

Blood

388 Norma! Whole 105 2.69043 134,5215 85,02 13 87,73 4.42 0.0048

Blood

389 Normal Whole 105 2.6952 134.76 87,3 4.46 0 -3 0.4521

Blood

390 Normal Whole- 105 2.87943 343.9715 83 .03 34.46 86.82 4.53 0.0048

Blood

391 Tumor Fresh 105 2.07478 303.739 35.85 33.24 87.58 4.6 0.0224

Frozen

Tissue

392 Tumor Fresh 105 2.65385 132.6925 55.08 12.25 87.86 4.53 0.0034

Frozen

Tissue

393 Normal Whole 105 2.25624 ! 32,812 47,76 1 3 .8 87,55 4.62 0.0033

Blood

394 Normal Whole- 105 2.84579 342.2895 42.4 32.33 87.23 4.53 0.009

Blood

393 Norma! Whole 105 2.97739 148.8695 51.29 11.59 86.04 4.6 0.0046

B!ood

396 Norma! ^"Whole 105 2.89612 144.806 67.39 12.95 88.65 4.46 0.0056

Blood

397 Norma! Whole 105 2.7863 2 139.306 69.58 13 88.05 4.4 0.0059

Blood

398 Norma! ^"Whole 105 2.92724 146.362 68.2 14.35 87.51 4.46 0.0041

Blood

399 Tumor Fresh 105 3.00034 i 50,017 50,5 12.31 88,36 4.49 0.0018

Frozen

Tissue

400 Tumor Fresh 105 2.93865 146.9325 51.49 11.99 88.63 4.5 0.0023

Frozen

Tissue

40 i Tumor Fresh 105 2.7392 135.96 44.02 12.26 88.11 4.58 0.0022

Frozen

Tissue

402 Normal Whole 105 2.05029 Ϊ 02, 5145 44,31 12.5 88,91 4.54 0.0042

Blood

403 Norma! ^"Whole 105 2.95087 147.5435 74.42 1 3.98 88.07 4.46 0.003

Blood

404 Norma! Whole 105 2.87887 143.9435 72.44 12.45 86.78 4.38 0.0038

Blood Penalty

Starting Target 20x of

Tumor materia! Input Bases EXEX % Normal type Vol Cone DNA (ng) T^Jond Pico Catch Pico 20% data Adapter

405 Tumor Fresh 105 2.21263 110.6315 48.6 12.07 88.27 4.49 0.004

Frozen

Tissue

406 Normal Whole 105 2.568 328.4 63 .07 34.26 87.38 4.51 0.0027

Blood

407 Tumor Fresh 105 2.17888 108.944 23.58 3 3.67 86.24 5.33 0.0026

Frozen

Tissue

408 Tumor Fresh 105 2.90591 145.2955 58.91 12.29 86.46 4.52 0.0027

Frozen

Tissue

409 Tumor Fresh 105 2.68043 134.0215 58,98 ! 1 ,75 87,99 4.59 0.0022

Frozen

Tissue

410 Tumor Fresh 105 2.11641 105.8205 44.84 9.86 85.48 4.7 0.0042

Frozen

Tissue

411 Normal Whole 105 2.88933 144.4565 69.48 12.32 87.3 4.52 0.0032

Blood

412 Normal Whole 105 2.4293 121 ,465 46,37 9.17 85,02 4.67 0.0076

Blood

413 Normal Whole 105 2.87028 Ϊ 43.514 76,09 ! 1 ,45 85,41 4.56 0.0035

Blood

414 Normal Whole 105 2.31304 3 35.652 50.77 32.53 88 4.44 0.0094

Blood

13 Tumor Fresh 105 2.76271 138.1355 65.04 12.95 85.02 4.7 0.0021

Frozen

Tissue

416 Tumor Fresh 105 2.76058 138.029 42.73 11.24 88.62 4.64 0.0025

Frozen

Tissue

417 Normal Whole 105 2.18075 309.0375 43.94 32.79 88.09 4.58 0.0034

Blood

418 Normal Whole 105 2.75988 337.994 65.79 32.36 87.93 4.56 0.0025

Blood

419 Normal Whole 105 2.68495 134.2475 74.32 13.28 86.31 4.53 0.0029

Blood

420 Norma! ^'Whole 105 2.7! 939 135.9695 59.15 12.72 87.42 4.63 0.0049

Blood

421 Normal Whole 105 2.74766 137.383 59.61 13.49 87.89 4.45 0.0033

Blood

422 Normal Whole 105 2.5416 127,08 74,33 13,32 85,21 4.67 0.0056

Blood

423 Tumor Fresh 105 2.8664 143.32 46,51 ! 1 ,44 86,52 4.82 0.0012

Frozen

Tissue

424 Normal Whole 105 2.1702 108.51 56.68 11.41 87.89 4.44 0.0033

Blood

425 Norma! ^'Whole 105 2.21 391 110.5955 39.99 12.07 88.64 4.52 0.0026

Blood

426 Tumor Fresh 105 2.19266 109.633 38.28 9.05 88.62 4.72 0.0048

Frozen

Tissue

427 Normal Whole 105 2.07371 103,6855 52,63 1 3 .81 87,78 4.52 0.0065

Blood

428 Normal Whole 105 2.2246 3 3 3.23 53.16 3 3.3 87.18 4.56 0.0077

Blood

429 Norma! Whole 105 2.73793 136.8965 55.27 12.42 87.45 4.53 0.0088

Blood

430 Norma! ^'Whole 105 2.7! 723 135.8605 74.42 13.52 87.22 4.47 0.0047

Blood

4 1 Norma! Whole 105 2.2992 114.96 74.02 12.89 82.87 4.62 0.0036

Blood Penalty

Starting Target 20x of

Tumor material Input Bases EXEX % Normal type Vol Cone DMA (ng) r^jond Pico Catch Pico 20% data Adapter

432 Normal Whole 105 2.03962 101.98! 51.96 12.31 87.68 4,37 0.0051

Blood

433 Normal Whole 105 2.21503 110,7515 56,87 10,5 87,38 4,59 0.0048

Blood

434 Normal Whole 105 2.83495 141 ,7475 73,19 1 3 .5 86,62 4.49 0.0012

Blood

435 Normal Whole 105 2.33165 1 36.5825 66.79 1 3.87 88.45 4.45 0.0044

Blood

436 Normal Whole 105 2.38662 119.331 62.7 12.67 87.86 4.51 0,0058

B!ood

437 Norma! ^'Whole 105 2.79 139.5 56.83 13.26 87.35 4.43 0.003

Blood

438 Normal Whole 105 2.82 141 71.69 14.02 86.48 4.58 0.0065

Blood

439 Tumor Fresh 105 2.86835 143, 175 66,57 12,27 87,08 4,56 0.0022

Frozen

Tissue

440 Tumor Fresh 105 2.72324 136.162 60.1 8 32.63 86.66 4.56 0.0029

Frozen

T'issue

44 i Tumor Fresh 105 2.80773 140.3865 49.36 10.89 85.46 4.74 0.0053

Frozen

Tissue

442 Normal Whole 105 2.78728 139,364 70,6 12,78 87,72 4,49 0.0018

Blood

443 Normal Whole- 105 2.84623 142.3115 78.87 30.95 88.45 4.39 0.003

Blood

444 Normal Whole 105 2.97213 148.6065 84.83 32.95 88.01 4.39 0,0027

B!ood

445 Normal Whole 105 2.83299 141.6495 70.02 14.37 85.9 4.46 0,0028

Blood

446 Norma! ^'Whole 105 2.53795 126.8975 73.18 13.31 86.85 4.54 0.0068

Blood

447 Normal Whole 105 2.13384 106.692 56.02 11.61 85.79 4.51 0.0047

Blood

448 Tumor Fresh 105 2.85228 142.614 41 ,1 12,22 86,35 4,56 0.0015

Frozen

Tissue

449 Normal Whole 105 2.19982 109.991 59.06 1 3.79 87.9 4.38 0,0029

Blood

450 Norma! Whole 105 2.80171 140.0855 66.9 12.62 86.38 4.53 0,0026

Blood

45 i Norma! Whole 105 2.86052 143.026 59.89 13.06 88.02 4.52 0.0034

Blood

452 Normal Whole 105 2.94668 147.334 69.65 13.68 85.72 4.56 0.0071

Blood

453 Normal Whole 105 2.78281 139,1405 74,87 12,89 88,52 4,52 0.0046

Blood

454 Normal Whole 105 2.75711 137,8555 63,56 13.43 87,4 4.47 0.0058

Blood

455 Normal Whole- 105 2.21196 1 10.598 53.39 32.62 87.4 4.5 0.0066

Blood

456 Norma! Whole 105 2.31683 115.8415 46.84 12.17 87.03 4.58 0.0084

B!ood

457 Norma! Whole 105 2.49067 124.5335 55.25 12.64 87.68 4.45 0.0103

Blood

458 Norma! Whole 105 2.88902 144.45 ! 68.17 12.56 87.23 4.4 0.0043

Blood

459 Norma! Whole 105 2.85276 142.638 65.29 13.25 87 4.49 0.0058

Blood

460 Normal Whole 105 2.83241 Ϊ 41 ,6205 55.94 1.3.32 88.45 4.55 0.0449

Blood Penalty

Starting Target 20x of

Tumor materia! Input Bases EXEX % Normal type Vol Cone DNA (ng) Pond Pico Catch Pico 20% data Adapter i Tumor Fresh 105 2.82075 141.0375 60.59 13.14 87.74 4.52 0.0336

Frozen

Tissue

2 Tumor FFPE 105 2.00087 100.0435 26.41 ! 3 .74 92.7 4.57 0.0026

Embedded

Block

3 Norma! Whole 105 2.16671 108.3355 74.36 13.56 93.15 4.59 0.0039

Blood

4 Normal Fresh 105 2.18562 109.28! 51.65 12.8 93.81 4.39 0.0034

Frozen

Tissue

5 Tumor FFPE 105 2.36036 Ϊ 18.018 55,39 1 .01 93 4.73 0.0018

Embedded

Block

6 Normal Whole 105 2.366 118.3 64.49 13.09 93.57 4.54 0.0031

B!ood

7 Tumor Fresh 105 2.40827 120.4135 66.46 14.16 92.71 4.49 0.0026

Frozen

Tissue

8 Tumor Fresh 105 2.44354 122,177 64.54 13,79 93,62 4.48 0.0031

Frozen

Tissue

9 Tumor Fresh 105 2.49759 124.8795 73.3 14.36 93.23 4.7 O.OfH

Frozen

Tissue

0 Tumor Fresh 105 2.63095 131.5475 71.5 13.5 93.83 4.43 0.0036

Frozen

Tissue

i Normal Whole 105 2.6897 Ϊ 34,485 76,37 1.3.34 93,7 4.47 0.0032

Blood

2 Tumor Fresh 105 2.70113 135.0565 75.23 14.38 92.74 4.84 0.0035

Frozen

Tissue

3 Norma! Whole 105 2.78028 139.014 74.29 13.97 93.58 4.48 0.0026

Blood

4 Tumor Fresh 105 2.783 36 139.058 74.03 13.54 93.09 4.71 0.0039

Frozen

Tissue

5 Normal Whole 105 2.80288 140,344 73,2.1 14.32 93, 19 4.45 0.0033

Blood

6 Normal Whole 105 2.93419 146.7095 73.63 14.43 93.63 4.47 0.0023

Blood

7 Norma! Whole 105 1.64638 82.319 65.2 14.4 91.44 4.62 0.0022

B!ood

8 Tumor Fresh 105 2.51696 125.848 65.8 13.51 92.9 4.82 0.0042

Frozen

Tissue

9 Tumor Fresh 105 1.56094 78.047 54,83 13,69 93,67 4.41 0.005

Frozen

Tissue

0 Norma! Whole 105 2.49428 124.714 60.55 13.66 94.04 4.4 0.0025

Blood

1 Tumor Fresh 105 2.40604 120.302 74.58 13.93 92.91 4.56 0.0022

Frozen

Tissue

2 Tumor Fresh 105 2.56701 128.3505 64.67 13.78 92.54 4.64 0.0036

Frozen

Tissue

3 Tumor Fresh 105 2.54288 127.344 62.45 13.34 93.93 4.54 0.0031

Frozen

Tissue

4 Norma! Whole 105 2.42525 121.2625 66.32 13.84 93.13 4.53 0.0062

Blood Penalty

Starting Target 20x of

Tumor materia! Input Bases EXEX % Normal type Vol Cone DMA (ng) T^Jond Pico Catch Pico 20% data Adapter

485 Normal Whole 105 2.30933 115.4565 67.52 14.38 91.26 4.59 0.027

Blood

486 Nonnai Fresh 54 2.22334 111 ,167 57,82 13,81 92,99 4.59 0.0049

Frozen

Tissue

487 Tumor Fresh 105 0.42666 23.333 3.04 5.33 0.11 -1 4.4608

Frozen

Tissue

488 Normal Fresh 54 2.05327 102.6635 57.29 13.69 93.51 4.56 0.0049

Frozen

Tissue

489 Normal Fresh 54 2.11818 Ϊ 05.909 61 .08 13.68 93.55 4.41 0.0031

Frozen

Tissue

490 Normai Fresh 54 1.7 85 54.9 13.31 93.32 4.51 0.0072

Frozen

Tissue

49 i Normal Fresh 54 1.13743 56.8715 34.06 13.21 93.33 4.36 0.0365

Frozen

Tissue

492 Normal Fresh 54 1 .58814 79.407 53 .33 14.03 93.91 4.32 0.005

Frozen

Tissue

493 Norma! Fresh 54 1.56733 78.3665 50.5 ■ ¾ ffl 92.87 4.5 0.0078

Frozen

Tissue

494 Normal Fresh 54 1.64331 82.1655 64.75 13.26 92.95 4.57 0.0055

Frozen

Tissue

495 Normal Fresh 54 1 .56199 78.0995 46.38 14.35 93.22 4.37 0.0106

Frozen

Tissue

496 Norma! Fresh 54 1.81447 90.7235 57.86 13.85 93.37 6.03 0.0041

Frozen

Tissue

497 Normal Fresh 54 2.03222 101.611 60,92 12,41 93,56 4.45 0.0046

Frozen

Tissue

498 Norma! Fresh 54 2.42461 123.2305 58 13.65 92.49 4.42 0.005

Frozen

Tissue

499 Norma! Fresh 54 2.50741 125.3705 60.01 13.3 93.44 4.51 0.0036

Frozen

Tissue

500 Normal Fresh 54 1 .60686 80.343 51 .51 ■3.73 93.83 4.34 0.0063

Frozen

Tissue

501 Norma! Fresh 54 1.59049 79.5245 45.64 12.81 93.42 4.4 0.0111

Frozen

Tissue

502 Normal Fresh 54 1.50824 75.412 44.62 12.96 91.33 4.47 0.0098

Frozen

Tissue

503 Normal Fresh 54 1 .68092 84.046 56.33 1 3 .16 93.24 4.77 0.0045

Frozen

Tissue

504 Norma! Fresh 105 2.76844 138.422 71.12 4.6 91.19 4.39 0.0039

Frozen

Tissue

505 Normal Fresh 105 3.04934 152,467 76,96 4.85 90,4 4.43 0.0026

Frozen

Tissue

506 Norma! Whole 105 2.58548 129.274 54.51 5.02 89.91 4.5 0.0024

Blood Penalty

Starting Target 20x of

Tumor material Input Bases EXEX % Normal type Vol Cone DNA (ng) T^Jond Pico Catch Pico 20% data Adapter

507 Normal Whole 105 2.1448 107.2 78.22 5.01 89.83 4.52 0.0015

Blood

508 Tumor Fresh 105 2.27565 113,7825 54,03 4.79 91,43 4.73 0.0045

Frozen

Tissue

509 Normal Whole 105 2.51171 125.5855 57.49 5.3 89.18 4.43 0.0078

B!ood

510 Normal Whole 105 2.86046 143.023 60.71 4.95 90.82 4,48 0.013

Blood

511 Norma! ^'Whole 105 2.96419 148.2095 75.36 5.25 90.39 4.44 0.0067

Blood

512 Normal ^"Whole 105 2.78886 139.443 74.06 5.43 90.1 4.43 0.0027

Blood

513 Normal Whole 105 2.42757 121 ,3785 64,88 5.22 90, 16 4.52 0.0025

Blood

514 Normal Fresh 105 3.344 167.2 80,23 5.36 90,41 4.47 0.0022

Frozen

Tissue

515 Normal Fresh 105 3.24007 162.0035 79.77 5.13 90.71 4,43 0.0017

Frozen

Tissue

516 Normal Fresh 105 2.88805 144.4025 82.5 5.17 90.2 4.4 0.0013

Frozen

Tissue

517 Tumor FFPE 105 3.07082 153.541 57.84 5.3 90.58 4.45 0.0022

Tissue

Section

518 Norma! ^"Whole 105 1.95172 97.586 54.83 5.37 90.33 4.44 0.0145

Blood

519 Tumor Fresh 105 2.73575 136.7875 41.8 5.18 91.38 4.56 0.0033

Frozen

Tissue

520 Normal Whole 105 1 .98398 99.199 59.51 4.94 90.95 4.44 0.0065

Blood

521 Normal Whole- 105 2.5677 128.385 73.19 5.33 90.97 4.47 0.0026

Blood

522 Norma! Whole 105 2.31727 115.8635 61.07 5.22 90.41 4.46 0.0024

B!ood

523 Tumor Fresh 105 1.75208 87.604 73.05 5.06 89.26 4.85 0.0038

Frozen

Tissue

524 Tumor Fresh 105 2.68685 134,3425 55,19 5.13 91,33 4.69 0.0027

Frozen

Tissue

525 Tumor Fresh 54 1.50187 75.0935 57.33 5.54 79.67 9.59 0.0027

Frozen

Tissue

526 Tumor Fresh 54 2.1633 2 108.156 78.47 5.21 90.23 4.53 0.0047

Frozen

Tissue

527 Tumor Fresh 54 2.60454 130.227 33.73 4.74 83.76 7.54 0.0364

Frozen

Tissue

528 Tumor Fresh 54 2.67641 133.8205 56.1 5.31 90.58 4,84 0.0018

Frozen

Tissue

529 Tumor Fresh 54 2.47819 123.9095 49.62 4.95 89.59 5.04 0.0034

Frozen

Tissue

530 Tumor Fresh 54 2.41003 120.50 : 5 49.03 4.9 9? ?6 5.0.3 0.0014

Frozen

Tissue Penalty

Starting Target 20x of

Tumor material Input Bases EXEX % Normal type Vol Cone DNA (ng) T^Jond Pico Catch Pico 20% data Adapter i Tumor Fresh 54 1.38756 69.378 50.42 5.23 88.83 4.82 0.0034

Frozen

Tissue

2 Tumor Fresh 54 2.16131 108.0655 59.55 4.81 89.88 4.95 0.0032

Frozen

Tissue

3 Tumor Fresh 54 2.57704 128.852 60.31 4.66 86.15 7.38 0.0019

Frozen

Tissue

4 Tumor Fresh 54 2.2670S 113,354 59,01 5,24 89,9 4.79 0.0032

Frozen

Tissue

5 Tumor Fresh. 54 2.13135 106.5675 55.81 4.92. 88.99 4.63 0.0085

Frozen

Tissue

6 Tumor Fresh 109 1.40555 70.2775 76.47 5.07 88.83 5.01 0.0064

Frozen

Tissue

7 Tumor Fresh 54 0.57662 28,831 13,47 5,32 88,95 4.98 0.0214

Frozen

Tissue

8 Normal Whole 105 2.05871 102.9355 49.98 5.26 90.32 5.07 0.0066

Blood

9 Tumor Fresh 109 2.73873 136.94 67.51 10.12886326 NA N 0.0087

Frozen

Tissue

0 Tumor Fresh 109 2.27709 113.85 69.71 9.03041921 NA NA 0.0037

Frozen

Tissue

S Normal Whole- 109 1 .81804 90.9 65.71 9.2.9758429 NA NA 0.0032

Blood

2 Normal Whole 109 2.39744 119.87 60.05 9.28502954 NA NA 0.014

Blood

3 Tumor Fresh 54 0.59841 29.92 6.17 7.379840433 NA NA 0.0873

Frozen

Tissue

4 Normal Fresh 105 2.89 144,26 66,11 15,19 92,73 4.18 0.002

Frozen

Tissue

5 Normal Fresh 105 2.69 134.54 56.9 15.22 93.31 4.19 0.0047

Frozen

Tissue

6 Normal Fresh 105 2.01 100.35 78.67 14.02 92.97 4.24 0.0032

Frozen

Tissue

7 Normal Fresh 105 2.43 121 .64 64,53 13.74 97 _. 4.12 0.0027

Frozen

Tissue

8 Normal Fresh 105 2.22 111.16 71.06 15.54 92.51 4,21 0.0044

Frozen

Tissue

9 Normal Fresh 105 2.6 130.15 65.83 15.74 92.73 4.15 0.0034

Frozen

Tissue

0 Normal Fresh 105 ? ¾7 1 18.7 66.64 15.28 91 .79 4.25 0.0025

Frozen

Tissue

1 Normal Fresh 105 2.3 115.15 61.95 17.18 90.73 4,21 0.0051

Frozen

Tissue

2 Normal Fresh 105 2.21 110.63 64.32 17.2 92_,33 4.17 0.0097

Frozen

Tissue Penalty

Starting Target 20x of

Tumor material Input Bases EXEX % Normal type Vol Cone DNA (ng) T^Jond Pico Catch Pico 20% data Adapter

553 Normal Fresh 105 2.4 120.08 64.01 15.79 91.46 4.33 0.0036

Frozen

Tissue

554 Tumor Fresh 54 2.12 106.23 58.26 13.38 93.69 4.23 0.003

Frozen

Tissue

555 Tumor Fresh 54 1.77 88.5 87.31 16.62 78.68 I i 0.0022

Frozen

Tissue

556 Tumor Fresh 54 1.83 91.71 85,45 16,13 92,36 4.43 0.0045

Frozen

Tissue

557 Tumor Fresh 54 1 .53 76.69 81 .82 14.82 72.36 14.33 0.0249

Frozen

Tissue

558 Tumor Fresh 54 2.36 118.23 74.19 14.95 91.71 5.09 0.0014

Frozen

Tissue

559 Normal Whole 105 2.82 140,98 60,92 13,52 91,81 4.22 0.0017

Blood

560 Normal Whole- 105 2.4 1 19.93 54.55 14.43 92.74 4.2 0.0049

Blood

561 Normal Whole 105 1.96 98.25 44.62 14.57 90.97 4.25 0.0059

Blood

562 Normal Whole 105 1.9 94.8 46.83 14.61 92.08 4.73 0.005

Blood

563 Norma! ^'Whole 105 2.1 104.75 51.31 15.33 92.18 4.29 0.0047

Blood

564 Normal ^"Whole 105 1.93 96.39 39.65 17.67 92.47 4.05 0.0065

Blood

565 Tumor Fresh 60 0.41064 20.532 1.73 11 ,97 82,41 8.15 0.0752

Frozen

Tissue

566 Tumor Fresh 60 1.66727 83.3635 2.61 10.5 71.76 -1 0.4721

Frozen

Tissue

567 Tumor Fresh 60 2.56634 128.317 18.74 10.69 93.09 4.34 0.0089

Frozen

Tissue

568 Tumor Fresh 60 1 .53753 76.8765 6.44 1 1 .88 90.68 4.71 0.0532

Frozen

Tissue

569 Tumor FFPE 60 1.99782 99.891 32.2 13.19 93.43 4.42 0.008

Embedded

Block

570 Normal ^"Whole 60 1.65041 82.5205 2.71 12.32 68.59 -1 0.0924

Blood

57Ϊ Normal Whole 60 4.4684S 223,424 51 ,77 16,79 92,71 4.35 0.0057

Blood

572 Normal Whole 60 3.85598 192,799 51 ,95 16,92 92,86 4.29 0.0044

Blood

573 Tumor Fresh 60 2.59215 129.6075 0.55 7.59 30.23 -1 0.9236

Frozen

Tissue

574 Tumor Fresh 60 2.12712 106.356 19.05 13.03 93.13 4.44 0.01 19

Frozen

Tissue

575 Tumor Fresh 60 4.06665 203,3325 3.26 11 ,05 84,41 0.1362

Frozen

Tissue

576 Tumor Fresh 60 3.57532 178.766 55.1 1 16.13 91.79 4.65 0.0047

Frozen

Tissue Penalty

Starting Target 20x of

Tumor material Input Bases EXEX % Normal type Vol Cone DMA (ng) Pond Pico Catch Pico 20% data Adapter

577 Tumor FFPE 60 1.20049 60.0245 19.1 12.95 91.81 4,55 0.0787

Embedded

Block

578 Normal Whole 60 1 .96788 98.394 33.6 14.34 92.59 4.22 0.008

Blood

579 Tumor Fresh 60 0.78238 39.119 2.93 1 3.58 84.95 6.96 0.1863

Frozen

Tissue

580 Tumor Fresh 60 4.48437 224.2185 26.07 12.86 93.9 4.87 0.0288

Frozen

Tissue

58 ϊ Tumor Fresh 61 1 .68878 84.439 93,82 12,08 89,54 4.65 0.0667

Frozen

Tissue

582 Normal Whole 114 2.0863 104.315 93.62 13.11 91.94 4.25 0.0076

Blood

583 Tumor Fresh 61 3.34839 167.4195 94.69 13.5 91.54 4.72 0.0037

Frozen

Tissue

584 Tumor Fresh 114 2.88544 144,272 91 ,88 12,45 88,87 5.33 0.0057

Frozen

Tissue

585 Normal Whole 61 0.8989 44.945 45.23 10.36 92.68 4.17 0.2445

Blood

586 Tumor Fresh 61 3.88221 194.1105 93.27 14.32 91.97 4.25 0.0051

Frozen

Tissue

587 Tumor Fresh 114 2.23268 111.634 85.51 14.84 90.26 5.27 0.0132

Frozen

Tissue

588 Tumor Fresh 61 1 .876 93.8 72.36 12.73 91.81 4.74 0.0029

Frozen

Tissue

589 Norma! ^'Whole 121 4.17647 208.8235 94.69 14.7 92.01 4.28 0.0032

Blood

590 Tumor Fresh 114 2.83032 141.516 95.1 14.37 89.87 5.13 0.0076

Frozen

Tissue

59 ϊ Tumor Fresh 70 4.65346 232,673 14,49 12,36 89,48 5.34 0.1942

Frozen

Tissue

592 Tumor FFPE 70 1.95 97.549 30.12 14.42 90.73 4.69 0.0183

Embedded

Block

593 Normal FFPE 70 2.34 117.0535 22.79 12.24 90.47 5.1 0.01 17

Embedded

Block

594 Normal FFPE 70 4.98 249.1635 82.88 13.42 9? ? 4.6 0.0038

Embedded

Block

595 Tumor FFPE 70 1.98 98.9345 22.43 11.51 92.06 4.29 0.0312

Embedded

Block

596 Tumor FFPE 70 3.78 189,0515 14.6 10,68 88,43 6.1 0.0363

Embedded

Block

597 Normal Whole 70 2.76971 138.4855 93.82 10.26 91.61 4.38 0.0125

Blood

598 Normal FFPE 70 3.9 195.211 74.76 12.93 90.59 4.68 0.0077

Embedded

Block

599 Normal FFPE 70 3.35 167.719 43.43 11.78 93.8 4.32 0.0044

Embedded

Block Penalty

Starting Target 20x of

Tumor material Input Bases EXEX % Normal type Vol Cone DNA (ng) Pond Pico Catch Pico 20% data Adapter

600 Tumor FFPE 70 2.59 129.683 55.85 11.83 93.27 4,5 0.0049

Embedded

Block

60S Tumor FFPE 70 2.78 138.7625 39.77 32.44 94.35 4.37 0.0203

Embedded

Block

602 Tumor FFPE 70 3.53 176.446 39.61 12.57 91.92 4.31 0.0307

Embedded

Block

603 Normal FFPE 70 4.26 213,089 48,55 12,78 94,04 4,23 0.0043

Embedded

Block

604 Tumor FFPE 70 4.13 206.7305 49.51 9.39 93.48 4.56 0.0214

Embedded

Block

605 Norma! FFPE 70 4.146 207.3 47.17 12.32 91.83 4.37 0.0046

Embedded

Block

606 Tumor FFPE 70 2.05509 102,7545 35,09 11 ,34 93,23 4, 18 0.0067

Embedded

Block

607 Tumor FFPE 70 3.22962 163.481 63.58 12.84 93.85 4.09 0.0055

Embedded

Block

608 Normal FFPE 70 3.83126 191.563 88.91 1 1.88 93.15 4.13 0.0034

Embedded

Block

609 Normal FFPE 70 4.38259 219,1 95 93 ,55 12,3 5 93,27 4.27 0.0021

Embedded

Block

610 Normal FFPE 70 3.96884 198.442 66.33 13.09 92.58 4.17 0,0038

Embedded

Block

61 i Tumor FFPE 70 2.92 145.8015 52.49 12.86 93.56 4,32 0.0361

Embedded

Block

612 Tumor FFPE 70 4.47324 223.662 66.97 32.77 92.52 4.25 0.0024

Embedded

Block

613 Tumor FFPE 70 3.7581 5 187.9075 45.67 11.32 93.85 4.1 0.0026

Embedded

Block

614 Normal FFPE 70 2.6096 130,48 42,71 11 ,46 93,53 4,33 0.0046

Embedded

Block

615 Normal FFPE 70 4.48342 224.171 67.65 1 3.11 94.21 4.08 0.0068

Embedded

Block

616 Tumor FFPE 70 2.86667 143.3335 70.67 13.12 89.67 5.25 0.003

Embedded

Block

617 Tumor FFPE 70 4.60954 230,477 73 ,86 12,3 5 93 ,76 4.33 0.0029

Embedded

Block

618 Normal FFPE 70 2.97011 148.5055 36.45 1 3.44 91.72 4.43 0,0071

Embedded

Block

619 Tumor FFPE 70 3.6071 5 180.3575 59.9 8.58 92.67 4.35 0.0239

Embedded

Block

620 Tumor FFPE 70 4 W 5 227,7825 53,2 12,78 93 ,6 4.46 0.0022

Embedded

Block Penalty

Starting Target 20x of

Tumor materia! Input Bases EXEX % Normal type Vol Cone DNA (ng) Pond Pico Catch Pico 20% data Adapter i Normal Whole 70 3.02801 151.4005 90.97 12.1 92.78 4.27 0.0017

Blood

2 Tumor Fresh 70 2.45335 122,6675 97,23 12,69 91,86 4.37 0.0013

Frozen

Tissue

3 Normal Whole 70 3.95717 197.8585 97.19 12.82 92.86 4.25 0.0019

B!ood

4 Normal Whole 70 2.14111 107.0555 90.14 11.85 92.85 4.22 0.0032

Blood

5 Norma! ^'Whole 70 4.65984 232.992 92.55 12.03 91.81 4.37 0.0016

Blood

6 Normal ^"Whole 70 4.40884 220.442 94.74 13.66 92.54 4.27 0.0037

Blood

7 Normal Whole 70 2.79225 139,6125 93,73 13,2 90,99 4.76 0.0022

Blood

8 Normal Whole 70 3.38336 169,168 89,6 1 .63 92,87 4.32 0.0021

Blood

9 Normal Whole- 70 3.91806 195.903 71 .25 13.1 8 91.42 4.5 0.0025

Blood

0 Normal Whole 70 4.61226 230.613 94.9 13.06 92.51 4.3 0.0013

Blood

i Norma! ^"Whole 70 4.58447 229.2235 95.3 12.66 93.24 4.24 0.0017

Blood

2 Norma! Whole 70 4.82796 241.398 93.73 13.59 93.09 4.27 0.0037

Blood

3 Norma! Whole 70 3.20383 160,1915 86,57 14,09 93,09 4.28 0.0104

Blood

4 Normal Whole 70 4.93813 246,9065 94,14 8.89 91 ,2 4.44 0.0426

Blood

5 Normal Whole- 70 3.48367 174.1 835 86.25 12.88 89.94 4.36 0.0025

Blood

6 Tumor Fresh 70 2.47009 123.5045 48.08 12.59 91.71 4.7 0.0105

Frozen

Tissue

7 Tumor Fresh 70 2.19604 109.802 91.43 12.75 91.66 4.81 0.0013

Frozen

Tissue

8 Tumor Fresh 70 2.36625 Ϊ 18,31 25 70,87 13.78 91 ,39 4.62 0.002

Frozen

Tissue

9 Tumor Fresh 70 3.76733 188.3665 29.95 13 91.37 4.95 0.0114

Frozen

Tissue

0 Norma! ^"Whole 70 1.68307 84.1535 26.54 11.79 91.92 4.37 0.0065

Blood

Ϊ Tumor Fresh 70 1.5173 75.865 10,26 9.6 91, 15 4.87 0.0658

Frozen

Tissue

2 Tumor Fresh 70 1 .43703 73.8515 4.94 8.81 69.54 -1 0.1188

Frozen

Tissue

3 Tumor FFPE 70 3.14066 157.033 64.84 12.31 92.52 4.28 0.002

Embedded

Block

4 Tumor FFPE 70 2.53618 126,809 29,93 Ϊ 1 ,49 93,7 4.14 0.0117

Embedded

Block

5 Norma! FFPE 70 3.15889 157.9445 34.99 11.85 94.03 4.17 0.0049

Embedded

Block

6 Tumor FFPE 70 3.05342 152.57! 43.27 12.82 92.48 4.2 0.0102

Embedded

Block Penalty

Starting Target 20x of

Tumor material Input Bases EXEX % Normal type Vol Cone DNA (ng) Pond Pico Catch Pico 20% data Adapter

647 Tumor FFPE 70 3.27039 163.5195 48.1 11.41 92.02 4,23 0.0205 mbedded

Block

648 Tumor FFPE 70 3.30392 165.196 38.54 10.76 95.01 4.03 0.0121

Embedded

Block

649 Tumor FFPE 70 3.14601 157.3005 ¾ ¾ 37 11.09 91 4.55 0.01 1 5

Embedded

Block

650 Normal Whole 70 3.46112 173,056 79,25 12,62 92,72 4.21 0.0019

Biood

651 Normal Whole 70 3.72786 186,393 93,42 13.71 92,56 4.3 0.0024

Blood

652 Tumor FFPE 70 2.28226 1 14.1 13 23.21 12.55 92.06 4.48 0.0079

Embedded

Block

653 Norma! ^'Whole 70 2.63946 131.973 81.35 13.72 92.06 4.31 0.0037

Blood

654 Normal Whole 64 3.23559 161.7795 94.83 1 1.77 92.48 4.34 0.0076

Blood

655 Normal Fresh 120 3.06703 153,3515 77,3 23,26 88,64 7.19 0.5887

Frozen

Tissue

656 Normal Whole- 120 3.09657 154.8285 71 .89 23.02 90.85 5.66 0.0934

Blood

657 Normal Whole 120 2.88996 144.498 62.1 27.52 88.86 5.56 0.156

B!ood

658 Norma! ^'Whole 120 3.09782 154.89! 61.61 25.1 92.17 6.36 0.1204

Blood

659 Norma! Whole 120 3.70408 185.204 74.9 22.68 91.98 6.07 0.1247

Blood

660 Norma! Whole 120 3.79432 189.716 68.2 24.91 87.95 5.73 0.1294

Biood

6 1 Normal Whole 120 3.39958 169,979 65,6 22,82 91 ,9 6.01 0.2774

Blood

662 Normal Whole- 120 3.33777 166.8885 84.79 26.87 90.84 6.62 0.0716

Blood

663 Norma! Whole 120 2.66343 133.1715 78.58 25.87 89.84 6.83 0.0828

B!ood

664 Norma! Whole 120 2.8181 140.905 83.27 25.18 90.97 6.14 0.0742

Blood

665 Norma! Whole 120 2.60002 130.00! 79.64 25.22 90.99 6.03 0.1041

Blood

666 Norma! Whole 120 3.60936 180.468 90.97 25.81 90.32 5.99 0.055

Biood

667 Norma! Whole 120 3.4512 172,56 91 ,34 24,62 90,47 6.35 0.0406

Blood

668 Normal Whole- 120 3.34512 167.256 78.97 24.23 89.74 6.31 0.1219

Blood

669 Norma! Whole 120 3.36273 168.1365 43.87 23.13 92.92 5.1 3 0.0891

Blood

670 Norma! Whole 120 2.85877 142.9385 68.53 41.67 89.54 5.58 0.0619

Blood

67 i Norma! ^'Whole 120 2.78859 139.4295 58.85 25.4 91.01 5.8 0.1636

Blood

672 Norma! Whole 120 3.12439 156.2195 78.42 24.22 87.7 8.29 0.0353

Blood

673 Norma! Whole 120 3.43112 171 ,556 88,45 22 89,93 6.02 0.0532

Biood

674 Normal Whole 120 3.66875 183,4375 90,42 21 ,78 90,41 5.83 0.0341

Blood

675 Normal Whole- 120 3.08167 154.0835 73.08 26 91.26 5.58 0.1961

Blood Penalty

Starting Target 20x of

Tumor material Input Bases EXEX % Normal type Vol Cone DNA (ng) T^Jond Pico Catch Pico 20% data Adapter

676 Normal Whole 120 3.05633 152.8165 82.23 32.45 90.66 5.73 0.0371

Blood

677 Normal Whole 120 3.57009 178,5045 78,47 23,34 89,45 6.11 0.0518

Blood

678 Tumor Ceil Line, 60 2.20399 1 10,1995 58,84 35,31 90,37 7.29 0.1418

Viable

679 Normal Cell Line, 120 3.13604 156.802 57.33 23.07 87.83 6.08 0.0504

Viable

680 Tumor Fresh 120 2.79986 139.993 90.39 22.08 90.01 6.23 0.0447

Frozen

Tissue

68 i Normal ^"Whole 120 2.58765 129.3825 89.7 32.17 90.25 5.48 0.04

Blood

682 Normal Whole 120 3.36233 168,1165 72,54 23,32 90,35 5.86 0.0754

Blood

683 Normal Whole 120 1 .65471 82.7355 52,89 23,3 88,06 6.48 0.0552

Blood

684 Tumor Cell Line, 60 2.66848 133.424 94.86 24.63 88.14 6 0.0527

Viable

683 Tumor Fresh 120 3.20583 160.2915 77.28 13.02 91.47 4.25 0.0254

Frozen

Tissue

686 Tumor Fresh 120 3.52797 176.3985 74.32 13.01 93.21 4.2 0.0032

Frozen

Tissue

687 Tumor Fresh 120 3.18936 159.468 87.34 12.93 93.16 4.35 0.0044

Frozen

Tissue

688 Tumor Fresh 120 3.08405 154.2025 84.51 12.69 92.73 4.72 0.006

Frozen

Tissue

689 Tumor Fresh 120 2.89329 144.5645 88.01 12.38 93.03 4.24 0.0043

Frozen

Tissue

690 Tumor Fresh 120 3.38715 169.3575 86.26 1 3 .85 93.61 4.48 0.0039

Frozen

Tissue

691 Tumor Fresh 120 3.13273 156.6365 80.13 10.78 93.06 4.34 0.0093

Frozen

Tissue

692 Tumor Fresh 120 2.97489 148,7445 79,26 15,19 92,45 4.28 0.0064

Frozen

Tissue

693 Tumor Fresh 120 3.45876 172.938 78.17 14.37 92.38 4.32 0.004

Frozen

Tissue

694 Tumor Fresh 120 3.07657 153.8285 82.29 14.57 92.47 4.38 0.0039

Frozen

Tissue

695 Normal Whole 120 3.41289 170.6445 86.54 14,34 94.79 4.23 0.0048

Blood

696 Tumor Fresh 120 3.45146 172.573 86.97 13.72 93.14 4.39 0.0025

Frozen

Tissue

697 Tumor Fresh 120 3.08009 154.0045 82.62 13.76 93.24 4.22 0.0025

Frozen

Tissue

698 Tumor Fresh 120 3.49434 174,717 85,32 14,4 91,22 4.46 0.0054

Frozen

Tissue

699 Tumor Fresh 120 3.35841 167.9205 74.99 12.59 92.73 4.24 0.0062

Frozen

Tissue Penalty

Starting Target 20x of

Tumor material Input Bases EXEX % Normal type Vol Cone DNA (ng) Pond Pico Catch Pico 20% data Adapter

700 Tumor Fresh 120 3.75099 187.5495 84.16 15.71 91.23 4.56 0.0033

Frozen

Tissue

70S Tumor FFPE 60 2.3445 1 17.225 56.49 13.06 87.03 6.23 0.2208

Embedded

Block

702 Norma! Whole 60 3.10808 155.404 87.48 13.5 91.16 5.21 0.008

Biood

703 Normal Whole 120 1.39832 69.916 90.88 14.07 93.65 6.87 0.01 18

Blood

704 Tumor FFPE 60 4.15827 207.9135 19 12.66 87.47 7.94 0.0201

Embedded

Block

705 Tumor FFPE 60 3.84366 192.1 83 83.83 14.2 89.7 5.68 0.0104

Embedded

Block

706 Tumor FFPE 60 3.12057 156.0285 22.19 13.38 88.15 6.84 0.0233

Embedded

Block

707 Normal FFPE 60 2.19991 109,9955 10,86 12,76 69,61 -1 0.1855

Embedded

Block

708 Tumor FFPE 60 5.43615 273.8075 19.81 14.27 85.35 8.79 0.0396

Embedded

Block

709 Tumor FFPE 60 3.93193 196.5965 29.01 12.02 89.19 7.06 0.0051

Embedded

Block

710 Normal FFPE 60 1 .31255 65.6275 17.34 1 1 .1 3 86.04 8.29 0.0155

Embedded

Block

711 Normal FFPE 60 4.63513 231.7565 88.26 14.09 75.37 -1 0.0679

Embedded

Block

712 Tumor FFPE 60 2.10037 105.0185 17.71 14.29 89.47 7.05 0.0217

Embedded

Block

713 Normal FFPE 60 1 .25115 62.5575 25.87 15.1 3 92.71 5.17 0.0138

Embedded

Block

714 Tumor FFPE 60 4.34614 217.307 92.39 16.69 90.8 6.36 0.0043

Embedded

Block

715 Tumor Fresh 60 3.86536 193.268 91.24 14.33 92.1 5.79 0.004

Frozen

Tissue

716 Normal FFPE 60 4.56534 228.267 88.16 16.22 92.16 5.72 0.0037

Embedded

Block

717 Tumor FFPE 60 4.13663 206.8315 90.72 16.6 92.01 6.09 0.0054

Embedded

Block

718 Tumor FFPE 60 2.7542 137,71 1 15,54 91 6.27 0.0034

Embedded

Block

719 Tumor Fresh 60 3.32444 166.222 93.05 15.63 91.48 5.77 0.0015

Frozen

Tissue

720 Normal FFPE 60 3.50944 175.472 78.85 14.07 92.84 5.52 0.0062

Embedded

Block

721 Normal FFPE 60 4.21531 210.7655 86.49 15.4 9? 4 5.4 0.0047

Embedded

Block Penalty

Starting Target 20x of

Tumor materia! Input Bases EXEX % Normal type Vol Cone DNA (ng) Pond Pico Catch Pico 20% data Adapter

722 Tumor FFPE 60 4.2275 211.375 89.65 15.29 92.09 5,88 0.003

Bmltedded

Block

723 Normal Whole 120 2.3844 1 39.22 85.8 33.26 90.8 4.4 0.3204

Blood

724 Normal Whole 120 2.20624 1 30.312 85.98 34.15 92.05 4.53 0.0341

B!ood

723 Normal Whole 120 2.33381 116.6905 88.22 14.76 91.57 5.15 0.0953

Blood

726 Norma! ^'Whole 120 2.75531 137.7655 87.72 15.53 90.92 6.38 0.0638

Blood

727 Normal Whole 120 2.07684 103.842 89.19 14 91.79 4,56 0.0568

Blood

728 Normal Whole 120 2.24306 112,153 85,22 1 90, 11 4.45 0.0941

Blood

729 Normal Whole 120 2.37144 Ϊ 18.572 86,32 14.26 92,33 4.47 0.0721

Blood

730 Normal Whole 120 2.15083 307.5415 84.58 36.09 93.26 5.58 0.1248

Blood

731 Normal Whole 120 2.02216 101.108 88.13 15.25 90.29 5.82 0.1042

B!ood

732 Norma! ^'Whole 120 2.23582 111.79! 88.55 13.78 92.42 4.36 0.0285

Blood

733 Norma! Whole 120 2.21978 i 10.989 83 15.48 91.15 5.54 0.2637

Blood

734 Normal Whole 120 2.18764 109,382 88,93 14,96 92,39 4.7 0.1133

Blood

735 Normal Whole 120 1 .83854 91.927 89,03 14.21 82,88 12.94 0.0325

Blood

736 Normal Whole 120 2.36581 3 38.2905 89.63 35.79 89.6 4.94 0.1775

Blood

737 Normal Whole 120 2.70756 335.378 90.91 34.53 91.76 4.38 0.0401

B!ood

738 Norma! ^'Whole 120 2.43026 121.513 82.9 15.7 90.68 6.25 0.1523

Blood

739 Norma! Whole 120 2.38507 119.2535 86.75 15.4 91.78 5.15 0.3604

Blood

740 Normal Whole 120 2.5102 125.51 84.72 15.41 91.41 6.54 0.2339

Blood

741 Normal Whole 120 2.07233 103,6165 80,86 14,56 91,94 4.79 0.0548

Blood

742 Normal Whole 120 2.26577 3 33.2885 94.53 34.03 92.45 4.33 0.0234

Blood

743 Normal Whole 120 2.41733 320.8665 93.87 33.56 92.21 4.42 0.0479

B!ood

744 Norma! Whole 120 2.44186 122.093 92.38 15.07 90.99 4.36 0.0087

Blood

745 Norma! ^'Whole 120 2.96377 148.0885 87.11 16.61 89.51 5.09 0.4095

Blood

746 Normal Whole 120 2.18389 109.1945 84.46 14.05 92.44 4.29 0.0329

Blood

747 Normal Whole 120 2.203 110,15 81 ,41 14,35 91,79 4.53 0.0661

Blood

748 Normal Whole 120 2.70692 !35,346 88,28 15.03 93 ,75 5.39 0.2004

Blood

749 Normal Whole 120 2.13804 306.902 80.69 34.06 90.49 5.8 0.1185

Blood

750 Norma! Whole 120 2.21483 110.7415 92.58 14.3 91.41 5.07 0.1159

B!ood

75 i Norma! ^'Whole 120 2.52969 126.4845 90.61 15.63 90.27 4.53 0.0249

Blood

752 Norma! Whole 120 2.2571 112.855 81.46 16.59 91.35 4.61 0.0704

Blood Penalty

Starting Target 20x of

Tumor material Input Bases EXEX % Normal type Vol Cone DNA (ng) Pond Pico Catch Pico 20% data Adapter

753 Normal Whole 120 2.03652 101.826 87.43 15.77 90.2 4,77 0.1266

Blood

754 Normal Whole 120 2.06625 103,3125 77,6 14.94 91,39 5,03 0.1942

Blood

755 Normal Whole 120 2.08115 104.0575 91 ,69 12.46 89,98 4.35 0.0166

Blood

756 Normal Whole 120 2.29073 1 34.5365 83.94 12.36 92.46 4.28 0,0489

Blood

757 Normal Whole 120 2.47936 123.968 88.98 13.7 89.85 5.58 0,0974

Blood

758 Norma! ^'Whole 120 2.89053 144.5265 90.7 13.96 91.94 4.7 0.0655

Blood

759 Normal Whole 120 2.19857 109.9285 90.96 14.75 91.06 4.75 0.0946

Blood

760 Normal Whole 120 2.41657 120,8285 87,21 14,58 91,59 4,44 0.0258

Blood

76 ϊ Normal Whole 120 2.06022 Ϊ 03 ,011 88,59 14.23 91 ,72 4.3 0.0256

Blood

762 Normal Whole- 120 1 .99552 99.776 77.1 7 12.52 92.48 4.26 0.0494

Blood

763 Normal Whole 120 2.04005 102.0025 85.57 14.49 91.3 5.53 0,2551

Blood

764 Norma! ^'Whole 120 2.14862 107.43 ! 82.42 14.01 90.08 5.26 0.1 3 56

Blood

765 Norma! Whole 120 2.49141 124.5705 90.54 13.7 90.81 4.3 0.057

Blood

766 Norma! ^"Whole 120 2.66859 133.4295 84.07 13.18 89.99 4,58 0.1009

Blood

767 Norma! Whole 120 2.21086 110,543 88,87 14.94 91,96 4,34 0.0149

Blood

768 Normal Whole- 120 2.57543 128.7715 90.1 3 14.79 91.79 4.39 0.0175

Blood

769 Normal ^"Whole 120 2.10686 105.343 80.33 14.44 92.18 4.33 0,0239

Blood

770 Norma! Whole 120 2.13833 106.9165 80.8 12.78 91.94 4.35 0,014

Blood

77 i Norma! ^'Whole 120 1.86236 93.118 84.96 12.6 92.51 4.43 0.0382

Blood

772 Norma! ^"Whole 120 2.36048 118.024 88.74 12.76 91.81 4,35 0.0343

Blood

773 Norma! Whole 120 2.49689 124,8445 90,29 13,69 90, 1 5,27 0.0437

Blood

774 Normal Whole 120 2.48667 124,3335 82,4 12.91 91 ,6 4.99 0.1158

Blood

775 Normal Whole- 120 2.40077 120.0385 91 .48 14.87 90.63 4.44 0.0275

Blood

776 Norma! Whole 120 2.22789 111.3945 88.27 14.84 90.8 4.36 0,0174

Blood

777 Norma! ^'Whole 120 2.16328 108.164 81.79 13.05 92.2 4.35 0.0291

Blood

778 Norma! Whole 120 2.31326 115.663 77.06 14.01 90.07 6.64 0.2099

Blood

779 Norma! ^"Whole 120 2.16092 108.046 85.52 11.49 92.01 4,54 0.0434

Blood

780 Normal Whole 120 2.3245 Ϊ 16,225 91 ,7 12.83 92.12 4.39 0.0275

Blood

78 S Normal Whole- 120 2.37696 1 18.848 88.73 13.53 91.24 5.72 0.2218

Blood

782 Norma! ^"Whole 120 2.16791 108.3955 90.64 13.79 90.69 5.96 0,2063

Blood

783 Norma! Whole 120 1.92946 96.473 83.58 14.91 90.22 5.14 0,3424

Blood

784 Norma! Whole 120 2.2127 110.635 79.88 13.3 89.4 4.45 0.022

Blood Penalty

Starting Target 20x of

Tumor material Input Bases EXEX % Normal type Vol Cone DMA (ng) Pond Pico Catch Pico 20% data Adapter

785 Normal Whole 120 2.003 39 100.0595 82.65 14.82 90.63 4.44 0.0755

Blood

786 Normal Whole 120 2.05335 102,6675 88,71 13,82 92,2 4.36 0.0169

Blood

787 Normal Whole 120 3.43643 171 .8215 96,33 12.55 93 ,95 4.38 0.0077

Blood

788 Normal Whole 120 2.30102 1 35.051 92.87 13.43 91.17 4.55 0.0239

Blood

789 Normal Whole 120 2.11126 105.563 87.4 14.52 90.06 5.14 0.4269

B!ood

790 Norma! ^'Whole 120 2.00335 100.1675 90.98 13.49 91.57 4.34 0.0099

Blood

79 i Normal Whole 120 2.30038 115.019 81.86 16.04 90.57 4.37 0.0393

Blood

792 Normal Whole 120 2.03982 101 ,991 84,06 13,58 92,05 4.35 0.0298

Blood

793 Normal Whole 120 3.57 178.5 90,1 7 13.1 j 90,32 4.55 0.024

Blood

794 Normal Whole- 120 3.49084 174.542 93 .87 13.97 90.78 4.68 0.0173

Blood

795 Normal Whole 120 0 0 2.88 5.3 0.03 -1 16.9992

B!ood

796 Norma! ^'Whole 120 0 0 3.21 9.78 0.02 -1 15.4382

Blood

797 Norma! Whole 120 0 0 2.3 4.59 0.01 -1 41.939

Blood

798 Norma! Whole 120 0 () 2.2 7.57 0.05 -1 13.9161

Blood

799 Norma! Whole 120 0 0 1.72 3.93 0,01 -1 59.9567

Blood

800 Normal Whole- 120 0 0 2.63 2.66 0.02 -1 48.5006

Blood

801 Normal Whole 105 1.8 92.0875 83.54 15.73 92.4 4.57 0.0583

Blood

802 Norma! Whole 105 2.2 111.7515 85.53 15.84 92.18 4.6 0.0224

Blood

803 Tumor FFPE 105 1.7 85.53 30.85 13.56 94.41 4.34 0.0778

Embedded

Block

804 Norma! Whole 105 1.6 77.811 87,1 14.24 90,59 4.59 0.0109

Blood

805 Tumor Fresh 1 .9 97.409 0.39 12.1 1 3 .71 -3 2.3274

Frozen

Tissue

806 Norma! Fresh 55 1 52.3525 0.76 11.85 0.66 -1 I.! 406

Frozen

Tissue

807 Norma! Whole 55 2.1 102.9095 83.99 15.74 91.37 4.7 0.0128

Blood

808 Tumor Fresh 55 1 .3 63.7 9.7 13.92 76.59 -3 1.4758

Frozen

Tissue

809 Norma! Fresh 55 0.6 31.0955 2.29 12.21 37.6 -1 0.8926

Frozen

Tissue

810 Tumor FFPE 55 1.7 87.2205 80.46 15.28 90.81 4.96 0.0109

Emb dd d

Block

81 i Tumor FFPE 55 1 10.065 75.49 15.01 90.67 0.0232

Embedded

Block

812 Tumor FFPE 55 2.1 106.841 62.22 14.34 91.24 4.92 0.0201

Embedded

Block Penalty

Starting Target 20x of

Tumor materia! Input Bases EXEX % Normal type Vol Cone DNA (ng) Pond Pico Catch Pico 20% data Adapter

813 Tumor FFPE 55 1.9 96.7205 66.95 16.92 88.91 5,23 0.0265 mbedded

Block

814 Tumor Fresh 55 0.8 38.464 3.25 13.2 39.1 -1 0.5892

Frozen

Tissue

815 Norma! Whole 55 2.2 111.3955 85.28 17 92.51 4.65 0.0377

Blood

816 Normal Fresh 55 100.1235 4.82 12.19 31.98 -1 2.691

Frozen

Tissue

817 Normal Fresh 0.2 Ϊ 0.614 0.09 10.68 0,46 -1 4.0978

Frozen

Tissue

818 Normal Whole 120 3.81929 190.9645 85.91 18.26 86.27 7.66 0.642

B!ood

819 Unknown FFPE 120 2.72603 136.3015 52.21 16.15 92.15 7.45 0.1249

Embedded

Block

820 Normal Whole 120 2.67512 133,756 84,3 17,7 89,95 7.81 0.103

Blood

82 ϊ Unknown FFPE 120 2.9426 147.] 3 49,77 17.26 92,28 7.41 0.0347

Embedded

Block

822 Tumor Fresh 120 3.1398 156.99 27.29 16.51 91.18 6.44 0.3323

Frozen

Tissue

823 Tumor Fresh 120 3.22895 161.4475 59.82 16.51 90.13 5,2 0.1754

Frozen

Tissue

824 Tumor Fresh 120 2.1883 109.4155 57.86 16.88 91.76 5.32 0.1837

Frozen

Tissue

825 Tumor Fresh 120 2.65216 132.608 83.03 19.54 88.66 8.79 0.0733

Frozen

Tissue

826 Normal Whole 120 3.20813 160,4065 83,38 17,79 89,66 7.92 0.078

Blood

827 Normal Whole 120 2.44183 Ϊ 22, 0915 86,08 18.5? 90,93 6.18 0.0584

Blood

828 Tumor Fresh 120 2.51142 125.571 47.44 17.06 89.7 9.03 0.3013

Frozen

Tissue

829 Norma! ^'Whole 120 2.54085 127.0425 87.62 19.81 90.96 6.89 0.087

Blood

830 Normal ^"Whole 120 3.07849 153.9245 86.61 17.29 91.99 5.99 0.0616

Blood

831 Normal Whole 120 2.76443 138,2215 85,94 18,58 89, 15 6.15 0.1229

Blood

832 Unknown FFPE 120 2.66026 Ϊ 33 ,013 51 ,1 16.61 93, 19 4.53 0.0365

Embedded

Block

833 Tumor Fresh 120 3.1115 155.575 45.63 17.51 90.25 8.85 0.2227

Frozen

Tissue

834 Tumor Fresh 120 2.87764 143.882 81.56 19.15 90.2 8.02 1.4663

Frozen

Tissue

835 Tumor Fresh 120 3.1068 155.34 59.51 17.1 90.47 8.35 0.1039

Frozen

Tissue

836 Unknown FFPE 120 2.93784 146.892 49.14 16.56 92.48 6.68 0.0422

Embedded

Block Penalty

Starting Target 20x of

Tumor material Input Bases EXEX % Normal type Vol Cone DNA (ng) Pond Pico Catch Pico 20% data Adapter

837 Normal Whole 120 3.0783 153.905 89.21 18.24 92.11 4.79 0.0841

Blood

838 Tumor Fresh 120 3.44311 172,1555 65,96 17,13 91,21 6.31 0.2106

Frozen

Tissue

839 Normal Whole 120 1.96658 98.329 74.58 16.39 91.89 4.63 0.0379

Blood

840 Unk ow FFPE 120 2.81178 140.589 66.45 19.71 87.31 7.91 0.425

Embedded

Block

841 Tumor Fresh 120 2.0899 104.495 49.22 16.77 91.45 6.35 0.1318

Frozen

Tissue

842 Tumor Fresh 120 2.36948 1 18.474 74.41 17.42 90.09 7.65 0.1775

Frozen

Tissue

843 Tumor Fresh 60 2.49588 124.794 81.22 17.67 89.93 7.99 0.2577

Frozen

Tissue

844 Tumor Fresh 60 2.00032 100,016 70,19 18,87 82,75 8.49 0.1399

Frozen

Tissue

845 Tumor Fresh 60 2.07809 103.9045 74.41 17.82 90.93 6.55 0.1487

Frozen

Tissue

846 Tumor Fresh 60 2.95317 147.6585 80 51 15.79 90.04 5.16 0.0276

Frozen

Tissue

847 Tumor Fresh 60 2.44139 122.0695 75,69 18,97 87,7 8.89 0.1301

Frozen

Tissue

848 Unknown FFPE 60 0.5262 26.31 23.94 17.01 87.36 10.83 0.5218

Embedded

Block

849 Normal ^"Whole 60 1.96667 98.3335 74.02 18.25 90.81 7.17 0.1683

Blood

850 Normal Whole 60 2.50788 125,394 75,06 16,57 90,01 4.94 0.0985

Blood

85 ϊ Normal Whole 60 2.60609 130,3045 84,09 17,02 92,04 5.48 0.0833

Blood

852 Unknown FFPE 60 3.30204 165.102 59.25 16.94 88.96 7.03 0.0558

Tissue

Section

853 Unknown FFPE 60 2.40098 120.049 36.28 16.71 90.51 7.36 0.0988

Embedded

Block

854 Normal Fresh 60 0.72831 36.4155 29,35 18,28 89,92 7.28 0.6645

Frozen

Tissue

855 Normal Fresh 60 0.20899 10.4495 5.26 14.32 86.66 8.73 6.0222

Frozen

Tissue

856 Normal Fresh 60 0.27405 13.7025 6.87 15.54 87.59 8.61 4.0276

Frozen

Tissue

857 Normal Fresh 60 0.21513 10.7565 4.25 15.6 82.21 16.68 5.8916

Frozen

Tissue

858 Normal Fresh 60 0.343 1 17.1755 7.53 17.12 86.19 9.32 1.638

Frozen

Tissue

859 Unknown FFPE 60 0.16596 8.298 7.83 14.81 86.25 7 17 2.053

Embedded

Block Penalty

Starting Target 20x of

Tumor material Input Bases EXEX % Normal type Vol Cone DNA (ng) Pond Pico Catch Pico 20% data Adapter

860 Unknown FFPE 60 2.81 348 140.574 56.21 15.5 92.67 4.45 0.0131

Embedded

Block

86 S Normal Whole 120 0.15011 7.5055 0.23 7.47 0.02. -1 2.2.1724

Blood

862 Unknown FFPE 60 0.16294 8.347 8.29 14.02 88.58 9.09 1.5597

Embedded

Block

863 Tumor Fresh 54 3.57555 178.7775 17.45 14.36 92.52 4.69 0.0035

Frozen

Tissue

864 Normal Whole 54 3.88301 194,3 505 15.75 16.3 92.29 4.42 0.0016

Blood

865 Tumor FFPE 54 3.63761 383 .8805 3 3 .77 35.4 93.01 4.56 0.0023

Embedded

Block

866 Norma! ^'Whole 54 4.01396 200.698 15.18 16.26 93.17 4.44 0.003

Blood

867 Tumor FFPE 54 3.8756 193.78 11.8 13.96 90.03 4.82 0.0146

Embedded

Block

%

% PF % PF Reads % %

% PF Reads Unique % PF Aligned % Strand Target

% % % Off Reads Aligned % PF Reads Unique in Pairs Selected Balance Bases

Chimeras Duplication Bait AP AP Reads Aligned Reads AP Bases AP at l OOX

1 0.7764 19.4167 9.74 94.45 98.99 94.45 92.16 77.06 99.31 90,26 50 0.65256

2 0.7472 15.2089 10.23 94.28 99.19 94.28 92.36 80.78 99.5 89,77 50 0.61552

3 2.7937 20.0233 13.35 93.56 96.14 93.56 88.99 76.33 97.78 86.65 ' 50.01 0.56578

4 0.7899 16.6543 1 3.16 94.2 98.93 94.2 91.94 79.43 99.37 88.84 50.01 0.60292

5 0.5039 18.0379 9.76 94.36 99.39 94.36 92.31 78.23 99.44 90.24 50 0.59566

6 0.5888 15.0593 9.77 93.61 99 93.61 92.03 80.43 99.27 90.23 50.01 0.5477

7 0.588 14.646 9.78 94.17 99.3 5 94.3 7 92.26 81.39 99.41 90.22 50.01 0.58044

8 0.7802 14.717 10. J 94.34 99.3 5 94.34 92.09 81.24 99.43 89.9 50 0.47774

9 1 .0212 14.9857 9.99 94.02 99.02 94,02 92.05 80.79 99.31 90.01 50 0.55859 i O 0.71 34 15.2 9.8 93.74 99.02 93,74 92.07 80.37 99.3 90.2 50 0.51367

11 3,4201 22.2363 10.94 93.81 95.7 93,81 88.24 74.62 97.28 89.06 50 0.58124

12 0,8489 16.9256 9.73 94.33 ' 99. if 94,33 92.22 ' 79.24 99.38 90.27 50 0.59128

13 0.9269 14.6657 10.01 93.35 98.71 93.35 91.45 ' 80.58 99.03 89.99 50.03 0.45415

14 0.7085 17.2428 10.29 94.29 98.92 94.29 92.05 ' 78.95 99.23 89.71 50 0.58669

15 0.8733 15.7386 9.83 94.04 98.92 94.0 91.98 80.14 99.23 90.17 50 0.61027

16 1.4813 20.7545 9.66 93.72 98.31 93.72 93 .28 75.47 98.93 90.34 50.03 0.56637

17 2.9012 21.3887 10.25 93.94 97.35 93.94 90.21 75.19 98.26 89.75 50.02 0.56433

IS 2.8158 19.0209 10.28 93.44 97.07 93.44 90.08 77.01 98.06 89.72 50.03 0.56978

1 0.5999 16.9232 9.9 94.38 98.83 94.38 93 .86 79.33 99.09 90.1 50.03 0.56205

20 0.6993 1 5.5285 9.51 93.52 98.82 93.52 93 .7 79.94 99.3 3 90.49 50.03 0.52429

21 0.7282 17.3712 9.79 94.25 98.92 94.25 91.73 78.8 99.24 90,21 50 0.60204

22 0.8163 16.2312 10.14 94.58 98.99 94.58 91.47 80.08 99.28 89.86 ' 50 0.54615

23 0.6595 14.7253 9.99 94.52 99.32 94.52 91.69 81.39 99.39 90.01 50.01 0.49725

24 0.6204 14.2179 9.84 94.02 99.06 94.02 91.45 81.47 99.33 90.16 50 0.45578

25 0.7012 17.1543 10.17 94.38 99.39 94.38 91.8 79.07 99.44 89.83 50.01 0.50155

26 0.7061 15.6289 9.54 93.79 99.3 5 93.79 91.67 80.02 99.4 90.46 50 0.54814

27 0.7874 16.1 1 1 1 9.57 93.96 99.03 93.96 91.95 79.74 99.29 90.43 50 0.55503

28 0.6484 14.4306 9.49 94.37 99.03 94,37 92.01 81.55 99.27 90.51 50.01 0.52526

29 1 .4416 25.174 9.64 93.93 97.57 93,93 90.43 71.76 98.54 90.36 50.01 0.63008

30 2,3512 24.1289 9.48 94,39 97.37 94,39 90.93 73.01 98.26 90.52 50 0.62491

31 2,2804 21.3745 9.89 93.88 97.58 93,88 90.62 75.1 98.41 90.11 50 0.50783

32 0,829 17.6044 9.6 93.87 ' 98.96 93,87 92.08 ' 78.3 99.23 90.4 50 0.57291

33 1.6377 23.3987 9.27 93.68 98.21 93.68 91.66 ' 73.06 98.81 90.73 50 0.59726

3 1.1055 25.8441 8.6 93.65 98.33 93.65 92.05 70.83 98.97 91.4 50 0.57917 5 4.151 26.1901 11.32 94.44 95.8 94.44 88.14 71.49 97.35 88.68 50 0.56094

36 2.1984 24.2283 9.68 94.16 97.21 94.16 90.13 72.81 98.39 90.32 50.03 0.573 1

37 0.6143 1 7.9547 9.63 94.08 99.06 94.08 92.05 78.13 99.33 90.37 50 0.56834

38 2.6073 22.6434 9.87 93.94 97.16 93.94 90.32 74.1 98.3 90.13 50 0.59272

39 0.6144 22.4239 9.1 94.61 98.52 94.61 93 .68 74.49 99 90.9 50 0.6763

40 1.5144 23.9374 8.8 93.39 97.41 93.39 91.49 72.57 98.4 91,2 50 0.55352

41 1.8302 21.6201 9.64 93.76 97.55 93.76 90.51 74.83 98.47 90,36 ' 50 0.56879

42 3.5214 24.6408 9.31 94.19 97.84 94.19 91.01 72.33 98.57 90.69 50.01 0.55773

43 2.4547 26.966 9.52 93.97 96.54 93.97 89.58 70.39 97.77 90.48 49.99 0.56416

44 0.6765 18.4291 9.49 93.76 98.88 93.76 91.82 77.49 99.16 90.51 50 0.56405

45 0.8288 15.9157 9.79 93.92 99.06 93.92 91.95 79.85 99.36 90.21 50 0.4903

46 0.7377 16.4144 9.94 94.43 98.8 94.43 91.45 79.83 99.07 90.06 50 0.49813

47 0.6617 17.521 5 9.76 93.96 98.97 93.96 91.94 78.45 99.29 90.24 50 0.54

48 0.5817 16.1853 10.01 93.95 98.96 93.95 91.89 79.63 99.25 89.99 50.01 0.54561

49 0.51 55 14.6366 9.54 93.58 99.24 93.58 92.08 80.74 99.48 90.46 50 0.48985

50 0,6018 16.9586 9. 1 94,26 98.75 94,26 91.75 79.19 99.05 90.49 50 0.52681

51 0,6175 17.05 1 9.4 94,06 ' 99.05 94,06 92.18 ' 78.92 99.31 90.6 50.01 0.53319

52 0.5128 15.3366 9.57 94.39 99.27 94.39 92.34 ' 80.71 99.5 90.43 50 0.53408

53 0.442 16.2587 9.53 94.04 99.19 94.0 92.25 ' 79.61 99.44 90.47 50 0.53853

5 4.3473 31.5151 11 94.18 94.69 94.18 87.16 66.88 96.58 89 49.97 0.49229

55 0.734 23.8803 8.78 94.1 98.76 94.1 92.69 72.82 99.34 93.22 50 0.5923

56 2.2066 20.2391 10.07 93.73 98.02 93.73 93 .34 75.98 98.64 89.93 50 0.58263

57 0.9492 21.9774 8.63 94.3 98.78 94.3 92.89 74.68 99.2 93 .37 50 0.59369

58 0.4111 1 8.9363 7.91 93.95 99.18 93.95 93.62 77.15 99.39 92.1 50 0.50344

59 17.3417 20.4404 18.41 93.79 92.38 93.79 85.85 76.65 94.31 81,59 50.04 0.32724

60 1.2429 29.3859 9.55 93.33 98.2 93.33 91.03 67.42 98.83 90,45 50 0.52208

61 31.0403 36.953 29.3 93.02 90.91 93.02 79.24 62.36 92.92 70.7 ' 50.16 0.09815 %

% PF % PF Reads % %

% PF Reads Unique % PF Aligned % Strand Target

% % % Off Reads Aligned % PF Reads Unique in Pairs Selected Balance Bases

Chimeras Duplication Bait AP AP Reads Aligned Reads AP Bases AP at l OOX

62 0.1973 17.4716 7.94 96.5 99.38 96.5 93.43 80.19 99.55 92,06 50 0.47402

63 0.2096 15.9462 7.71 96.41 99.32 96.41 93.27 81.59 99.48 92,29 50 0.52855

64 0.3825 10.3997 8.04 96.56 99.15 96.56 92.43 86.93 99.38 91.96 ' 50 0.42719

65 3.9216 11.883 8.35 96.65 97.95 96.65 91.4 85.73 98.6 91.65 49.99 0.32838

66 3.2335 14.5465 8.99 96.71 96.03 96.71 89.26 83.5 97.48 91.01 49.98 0.25925

67 0.3593 11.3041 8.02 96.54 99.33 96.54 92.53 86.08 99.4 91.98 50 0.51878

68 0.3162 10.9536 7.69 96.54 99.36 96.54 92.77 86.43 99.41 92.31 49.99 0.52886

69 0.3342 10.7242 7.85 96.64 99.23 96.64 92.49 86.69 99.46 92.15 50 0.45743

70 0.3307 10.7849 7.93 96.66 99.2 96.66 92.47 86.65 99.48 92.07 50 0.47721

71 0.3364 37.7377 7.9 96.4 98.09 96.4 91.11 61.34 98.95 92.1 50 0.474

72 0,1997 29.5904 8.56 96.59 99.13 96,59 92.17 68.76 99.43 91.44 50 0.25837

73 0,8858 6.8703 48.65 96.69 ' 97.66 96,69 91.39 ' 90.35 99.3 51.35 50 0.31083

74 0.8593 4.5684 35.81 98.9 98.19 98.9 91.58 ' 94.51 99.35 64.19 50 0.09681

75 0.9448 7.8477 42.41 96.92 98.1 96.92 91.87 ' 89.62 99.41 57.59 50 0.35715

76 0.4464 14.1822 9.23 95.09 98.79 95.09 92.08 82.24 99.05 90.77 50 0.58617

77 0.4765 1 5.5389 9.43 95.07 99.03 95.07 92.49 80.96 99.27 90.57 50 0.57833

78 0.6501 1 5.4679 9.64 94.36 98.84 94.36 92.08 80.52 99.09 90.36 50 0.63292

79 0.5357 1 5.5042 9.78 95.04 98.85 95.04 92.17 81 99.36 90.22 50.03 0.53992

80 0.4916 1 .8979 9.45 94.57 98.69 94.57 93 .72 83.02 98.95 90.55 50.02 0.50927

81 0.5244 14.9276 9.32 94.87 98.83 94.87 93 .76 81.39 99.05 90.68 50 0.59386

82 0.3828 15.5027 9.19 95.08 98.92 95.08 92.1 81.01 99.16 90,81 50 0.60774

S3 0.4359 15.6334 8.78 94.39 98.79 94.39 92.31 80.39 99.05 91,22 ' 50.01 0.54751

84 0.4349 14.6694 10.02 94.55 98.92 94.55 92.11 81.38 99.21 89.98 50 0.56636

85 0.3994 14.1881 9.72 95.3 98.86 95.3 91.9 82.4 99.11 90.28 50.01 0.57784

86 0.5699 14.9732 9.29 94.82 98.92 94.82 92.16 81.33 99.16 90.71 50.01 0.59508

87 0.4809 14.8355 9.32 94.44 98.82 94.44 92.06 83.34 99.08 90.68 50 0.54533

88 0.5931 16.4285 9.26 94.78 98.63 94.78 91.75 79.97 98.91 90.74 50 0.55865

89 0,51 13 15.6453 9.3 95.09 98.75 95,09 91.95 80.93 99.06 90.7 50.01 0.58228

90 0,61 8 13.8543 9.38 94.54 98.87 94,54 92.52 82.32 99.14 90.82 50.01 0.54534

91 0,5134 14.2061 9.87 94.72 98.76 94,72 91.92. 1.94 99.05 90.13 50.01 0.45661

92 0,4934 13.031 9.32 94,34 98.77 94.34 91.71 82.72 99.01 90.68 50.02 0.49637

93 0,4273 15.4692 9.29 94.66 ' 98.85 94,66 91.93 ' 80.74 99.12 90.71 50 0.55499

9 0.5295 15.7291 9.4 95.16 98.53 95.16 91.47 ' 80.92 98.77 90.6 50.03 0.60113

95 0.3891 14.2411 9.62 94.57 98.72 94.57 91.94 81.81 99.06 90.38 50 0.53426

96 0.4503 3 3.2284 9.34 94.55 98.88 94.55 92.38 82.69 99.3 3 90.66 50 0.55407

97 0.735 3 3.5253 9.84 94.3 98.63 94.3 93 .73 82.25 98.9 90.16 50.02 0.50977

98 0.7 1 3 5.9221 9.04 94.29 98.43 94.29 93 .63 80.09 98.83 90.96 50 0.54409

99 0.6946 3 8.3458 9.09 94.92 98.5 94.92 93 .62 78.34 98.86 90,91 50 0.55737

100 0.4451 36.3023 9.22 95.2 98.81 95.2 93 .96 80.39 99.06 90,78 50 0.63229

101 0.4502 15.1574 9.2 95.21 98.9 95.21 92.12 81.43 99.15 90,8 50 0.58155

102 0.2929 23.3061 9.02 94.54 98.71 94.54 92.33 73.54 99,01 90.98 ' 49.99 0.6277

103 0.4155 12.3291 9.46 94.68 98.91 94.68 92.02 83.62 99.15 90.54 50 0.48001

104 0.5928 16.3294 9.44 95.2 ί 98.83 95.21 92.01 80.36 99.14 90.56 50.01 0.58527

105 0.5081 12.648 9.26 94.79 98.92 94.79 92.34 83.43 99.16 90.74 50 0.55965

106 0.346 14.2267 8.36 94.44 98.95 94.44 92.53 83.7 99.17 91.64 50 0.56563

107 0.4619 15.7283 9.33 94.98 98.74 94.98 91.89 80.76 98.97 90.69 50.01 0.57496

108 0.4582 28.998 9.47 94.9 98.87 94,9 91.91 68.45 99.12 90.53 50 0.7887

109 0.3716 14.5926 9.53 95.22 98.58 95,22 91.67 82 98.97 90.49 50.01 0.54997

1 10 0.5408 14.7759 9.36 94.68 98.74 94,68 91.88 81.38 99.03 90.84 50 0.50378

111 0,657 15.5829 9.38 94.69 98.69 94,69 91.93 80.68 98.94 90.62 50 0.56368 ill 0,6673 13.825 Ϊ 9.83 94.48 ' 98.85 94,48 92.18 ' 82. ί 99.1 90.17 50.01 0.48458

113 0.4864 13.8118 9.42 94.39 99.02 94.39 91.94 ' 82.02 99.27 90.58 50 0.46686

114 0.4466 16.0485 9.36 94.88 98.81 94.88 91.86 ' 80.39 99.07 90.64 50.03 0.56548

115 0.4356 15.8155 9.48 94.86 98.71 94.86 91.86 80.59 99.05 90.52 50.03 0.59307

116 0.5869 36.1403 9.31 95.43 98.86 95.41 92.08 80.68 99.33 90.69 50 0.58826

117 0.6496 3 5.4697 9.99 95.08 98.54 95.08 93 .55 81.09 98.84 90.01 50.03 0.49256

118 0.4967 3 7.7036 9.27 94.9 98.81 94.9 92.18 78.88 99.08 90.73 50 0.63243

119 0.4174 3 5.5106 9.22 94.54 98.75 94.54 93 .83 80.62 98.97 90.78 50 0.57951

120 0.5259 16.4871 9.24 94.77 98.58 94.77 91.85 79.93 98.87 90,76 50.01 0.56593

121 0.4041 17.5632 9.28 95.11 98.63 95.11 91.74 79.19 98.89 90,72 50.01 0.61318

122 0.4329 14.997 9.29 94.23 98.77 94.23 91.88 80.85 99.05 90.71 ' 50.01 0. 1722 %

% PF % PF Reads % %

% PF Reads Unique % PF Aligned % Strand Target

% % % Off Reads Aligned % PF Reads Unique in Pairs Selected Balance Bases

Chimeras Duplication Bait AP AP Reads Aligned Reads AP Bases AP at l OOX

123 0.4733 15.2009 9.33 94.77 98.79 94.77 92.06 81.07 99.06 90,67 50.01 0.54671

124 0.524 13.7923 9.24 95.04 98.78 95.04 92.08 82.57 99.02 90,76 50.01 0. 1682

125 0.6019 16.5397 9.01 94.97 98.64 94.97 91.76 80.02 98.89 90.99 ' 50.01 0.61186

126 0.4953 14.2545 9.39 94.49 98.71 94.49 91.82 81.73 98.96 90.81 50.01 0.54461

127 0.5354 15.6245 9.38 94.59 98.85 94.59 92.03 80.54 99.11 90.62 49.99 0.55045

1 28 0.7044 13.4044 9.67 94.98 98.41 94.98 91.46 82.93 98.72 90.33 50 0.53562

1 29 0.3856 15.5633 9.9 94.62 98.77 94.62 91.66 80.62 99.03 90.1 50.01 0.49956

1 0 0.6076 12.9808 9.37 94.43 98.95 94.43 92.33 82.82 99.28 90.63 50.01 0.507

1 31 0.3698 47.9858 4.69 94.67 14.98 94,67 8.1 87.88 80.72 95.31 49.88 0.03224

1 32 0.7547 17.0308 8.9 95.12 98.67 95,3 2 91.79 79.65 99.01 91.1 50 0.52708

133 1 ,6068 21.4236 90.1 94.34 96.32 94.34 89 75.4 98.46 9.9 50 2.00E- 05

1 34 0.6609 9.2916 93.71 94.99 95.68 94.99 89.37 86.78 98.5 6.29 50 1.00E- 05

135 0.7006 25.5492 93.94 94.69 97.34 94.69 91.11 71.8 99 8.06 50 5.00E- 05

136 1.1664 17.3269 93.29 94.23 96.75 94.23 90.35 78.92 98.65 6,71 50 2.00E- 05

137 0.351 Ϊ 16.8142 9.12 95.08 98.96 95.08 92.09 79.81 99.37 90,88 50 0.63903

138 0.4214 34.5362 8.38 94.67 97.4 94.67 90.47 63.69 98.36 91 .62 49.99 0.59641

139 0.6654 1 .5014 9.47 94.19 98.77 94.19 93 .67 83.06 99.08 90,53 50 0.52213

140 0.6595 14.4195 9.38 94.2 98.76 94.2 91.93 81.35 99.03 90,62 50.01 0.53951

141 0.5722 15.0931 10.07 94.82 98.61 94.82 91.7 81.23 98.91 89.93 ' 50.01 0.57619

142 0.288 77.1557 8.91 94.16 97.34 94.16 83.44 24.29 98.39 91.09 50 0.07872

143 0.2519 75.4792 8.44 94.23 94.22 94.23 74.01 27.93 97.15 91.56 49.99 0.12928

144 0.4059 32.4192 8.41 94.48 97.29 94.48 90.42 65.54 98.29 91.59 49.98 0.58149

145 0.7309 11.7882 9.67 94.23 98.63 94.23 91.58 83.75 98.92 90.33 50.01 0.53328

146 0.8445 13.321 1 9.46 95.01 98.7 95.01 92.04 82.98 98.96 90.54 50.01 0.58617

147 0.557 14.762 9.43 95.13 98.78 95,3 3 91.96 81.75 99.05 90.57 50 0.6185

148 0.2863 74.3429 8.41 94.65 97.53 94,65 85.83 26.74 98.49 91.59 50.01 0.0683

149 0,2409 47.2183 7.97 93.67 94.16 93,67 83.65 53.05 97.1 92.03 49.99 0.0459

150 0,408 24.4324 11.69 94.76 99.03 94,76 91.75 72.61 99.54 88.31 50 0.5568

151 0,35 13.2932 9.25 95.03 ' 99.26 95,03 92.36 * 82.95 99.49 90.75 50 0.41134

152 0.372 22.9618 9.19 95.05 99.42 95.05 92.51 ' 74.07 99.65 90.81 50 0.66219

153 0.3895 19.4016 11.43 94.4 99.09 94.4 91.99 76.96 99.48 88.57 50 0.5724

154 0.4828 20.6932 9.28 94.33 99.17 94. 1 92.01 75.7 99.43 90.72 50 0.60652

155 0.3916 20.1473 9.06 95.05 99.14 95.05 91 .98 76.71 99.38 90.94 50 0.62489

156 0.439 Ϊ 40.2117 10.58 91.76 99.07 91.76 93 .82 56.7 99.38 89,42 50 0.83665

157 0.3862 21.6296 9.35 94.56 99.19 94.56 93 .91 75 99.39 90,65 50.03 0.57336

158 0.2904 22.4228 9.16 94.76 99.27 94.76 92.28 74.4 99.48 90,84 50 0.63401

159 0.3085 22.2027 8.7 94.99 99.38 94.99 92.41 74.72 99.59 91.3 50 0.40061

160 0.3042 21.0826 9.04 94.3 99.22 94.3 92.2 75.33 99.45 90.96 ' 50 0.59182

161 0.2713 22.2432 8.73 94.52 99.35 94.52 92.36 74.4 99.58 91.27 50 0.62476

162 0.3259 20.8454 8.8 95 99.31 95 92.48 76 99.53 91.2 50 0.61769

163 0.2862 21.5888 8.94 94.78 99.32 94.78 92.48 75.38 99.55 91.06 50 0.61553

164 0.373 21.1637 9.07 94.68 99.22 94.68 92.23 75.53 99.46 90.93 50 0.62803

165 0.3479 20.8834 9.07 94.39 99.39 94.39 92.22 75.57 99.44 90.93 50 0.59568

166 0.4583 23.7232 9.3 94.74 99.07 94,74 92.07 73.22 99.34 90.9 50 0.64204

167 0.4672 21.8943 9.34 94.95 99.23 94,95 92.32 75.02 99.47 90.86 50 0.62412

168 0.4018 17.9132 8.82 93.9 99 9.3.9 92.23 77.96 99.21 91.18 50.01 0.5208

169 0,3916 23.7537 9.21 94.95 99.13 94,95 92.09 73.32 99.38 90.79 50 0.66575

170 0,4682 21.6193 9.15 94.9 Ϊ ' 99.23 94,91 92.04 ' 75.23 99.47 90.85 50 0.62012

171 0.3181 18.1805 8.82 95.03 99.21 95.01 92.19 ' 78.48 99.49 91.18 50 0.30846

172 0.3353 23.0115 9.17 94.74 99.23 94.74 92.18 73.85 99.49 90.83 50 0.63364

173 0.3853 1 8.3283 8.91 94.26 99.11 94.26 91 .93 77.83 99.37 91.09 50.03 0.47549

174 0.4245 39.9777 9.58 94.85 99.18 94.85 92.21 76.72 99.49 90.42 50 0.5634

175 0.3405 20.9752 9.01 94.53 99.28 94.53 92.33 75.57 99.55 90.99 50 0.62457

176 0.4262 25.1796 9.18 95.14 99.01 95.14 93 .55 72.13 99.27 90,82 50 0.64096

177 0.4895 19.937 12.85 94.54 98.99 94.54 92.11 76.57 99.43 87, 15 50 0.5933

178 0.388 16.9683 9.23 94.47 99.12 94.47 91.84 79.2 99.39 90,77 50 0.56151

179 0.3562 20.5838 9.11 94.22 99.18 94.22 92.24 75.74 99.43 90,89 50 0.57132 %

% PF % PF Reads % %

% PF Reads Unique % PF Aligned % Strand Target

% % % Off Reads Aligned % PF Reads Unique in Pairs Selected Balance Bases

Chimeras Duplication Bait AP AP Reads Aligned Reads AP Bases AP at l OOX

180 0.3758 21.4947 9.13 94.92 99.14 94.92 92.04 75.37 99.4 90,87 50 0.62688

181 0.4282 23.1234 9.12 95.13 99.13 95.13 92.19 74.01 99.39 90,88 50 0.64641

182 0.3853 18.8259 8.99 95.12 99.21 95.12 92.41 77.95 99.48 91.01 ' 50 0.58518

183 0.4519 33.5451 10.23 91.39 98.99 93.39 91.73 62.5 99.31 89.77 50 0.78408

184 0.3172 20.4285 9.58 94.79 99.28 94.79 92.17 76.25 99.51 90.42 50 0.58189

1 85 0.31 85 21.8551 9.3 95.09 99.33 95.09 92.17 75.33 99.57 90.7 50 0.58794

1 86 0.3392 21.8152 9.37 94.57 99.25 94.57 92.1 74.84 99.52 90.63 50 0.58673

1 87 0.3452 21.1052 8.93 94.71 99.22 94.71 92.25 75.57 99.48 91.07 50 0.64734

1 88 0.3436 20.5947 9.28 94.35 99.24 94.35 92.16 75.82 99.49 90.72 50 0.5524

1 89 0.3732 23.6805 9.48 95.03 99.08 95.03 91.82 73.44 99.35 90.52 50 0.51084

190 0,4094 38.7637 9.86 90.94 99.05 90,94 91.92. 57.64 99.34 90.14 50 0.81089

191 0.354 22.4148 9.66 95.23 ' 99.18 95,23 92.21 ' 74.7 ί 99.42 90.34 50 0.62324

192 0.3724 18.5937 9.2 94.63 99.22 94.61 92.09 ' 77.81 99.46 90.8 50 0.52638

193 0.4456 22.5584 9.47 94.53 99.08 94.51 91.8 ' 74.14 99.34 90.53 50 0.61944

194 0.4125 24.5842 9.69 94.63 99.19 94.63 91.85 72.34 99.46 90.31 50 0.59392

195 0.4705 22.9048 9.43 94.35 99.15 94.35 92.1 73.71 99.43 90.57 50 0.59625

196 0.4009 J 7.8719 9.51 94.33 99.31 94.33 92.22 78.26 99.57 90.49 50 0.56896

197 0.4334 38.9254 10.15 90.83 99.06 90.83 93 .79 57.4 99.34 89.85 50 0.79401

198 0.459 19.8354 11.51 94.8 98.95 94.8 93 .94 76.85 99.46 88.49 50 0.56787

199 0.2845 20.9322 9.24 95.36 99.32 95.36 92.35 76.15 99.53 90.76 50 0.59664

200 0.3216 25.1923 9.38 95.07 99.13 95.07 92.33 72.07 99.34 90,62 50 0.58904

201 0.277 24.8065 10.38 94.97 99.19 94.97 92.09 72.35 99.48 89,62 ' 50 0.60653

202 0.2991 24.9083 9.31 94.45 99.38 94.45 92.16 71.92 99.41 90.69 50 0.62069

203 0.2983 22.6689 9.3 1 94.67 99.33 94.67 92.1 74, 33 99.35 90.89 50 0.61232

204 0.3187 24.173 9.69 95.16 99.05 95.16 92.01 73.08 99.32 90.31 50 0.6296

205 0.41 81 19.2295 9.92 94.69 99.3 94.69 91.9 77.29 99.41 90.08 50 0.54715

206 0.3539 20.8351 9.41 95 99.33 95 91.97 76.02 99.35 90.59 50 0.5433

207 0.3993 23.3579 9.51 94.94 99.04 94,94 91.92 73.68 99.27 90.49 50 0.6039

208 0.3512 24.1446 9.26 94.45 99.04 94,45 92 72.65 99.29 90.74 50 0.61992

209 0,3671 22.0987 9.9 94.55 99.3 94,55 92.37 74.55 99.54 90.1 50 0.58006

210 0,3657 24.1852 9.69 95.04 98.97 95.04 91.76 72.99 99.23 90.31 50 0.37323

211 0,3979 41.0524 9.86 90.93 ' 99,03 90,93 91.41 ' 55.62 99.3 90.14 50 0.58854

212 0.3243 21.0834 13.11 94.63 98.78 94.61 91.7 ' 75.61 99.39 86.89 50 0.57583

213 0.336 20.3157 9.08 94.3 99.39 94.3 92.31 76 99.6 90.92 50 0.56338

214 0.3484 23.0331 9.39 95.09 99.1 95.09 92.14 74.07 99.33 90.61 50 0.60082

215 0.3644 23.2928 9.05 94.73 99.24 94.73 92.37 73.58 99.46 90.95 50 0.58739

216 0.3193 24.5599 9.39 95.06 99.34 95.06 92.31 72.59 99.58 90.61 50 0.59838

217 0.2671 23.6652 9.28 94.73 99.36 94.71 92.27 73.2 99.58 90.72 50 0.63 3 78

218 0.3779 23.1327 11.47 95.14 98.9 95.14 93 .75 74.06 99.35 88.53 50 0.60505

219 0.3008 25.1712 10.72 94.4 99.04 94.4 91.62 71.7 99.44 89,28 50 0.59161

220 0.2946 21.6126 9.44 94.97 99.29 94.97 92.01 75.26 99.53 90.56 ' 50 0.27535

221 0.3465 19.1401 9.21 94.65 99.05 94.65 91.77 77.36 99.35 90.79 50 0.17842

222 0.288 24.9452 9.49 94.97 99.26 94.97 92.07 72.2 99.47 90.51 50 0.59685

223 0.3382 22.1167 9.36 94.08 99.21 94.08 92.05 74.23 99.43 90.84 50 0.53894

224 0.3406 22.4771 9.38 94.04 99.2 94.04 92.23 73.89 99.44 90.62 50.01 0.53632

225 0.4769 23.9959 17.62 94.75 98.39 94.75 90.84 73.35 99.23 82.38 50.01 0.49512

226 0.4954 40.9383 19.39 90.56 98.27 90.56 90.69 55.77 99.15 80.61 50 0.76268

227 0.286 24.5825 10.28 94.77 99.25 94,77 92.25 72.42 99.52 89.72 50 0.6318

228 0.2877 20.6692 9.58 94.25 99.36 94,25 92.23 75.67 99.41 90.42 50 0.54719

229 0,3803 22.8366 9.5 95.02 99.19 95,02 92.29 74.18 99.42 90.5 50 0.5866

230 0,3641 24.6038 9.38 95.1 ' 99.25 95.1 92.32 ' 72.6 99.52 90.62 50 0.65057

231 0.32 20.62 9.6 94.94 99.26 94.9 92.08 ' 76.17 99.53 90.4 50 0.59888

232 0.3696 21.1759 9.68 94.1 99.11 94.1 91.81 ' 7S. il 99.37 90.32 50 0.53868

233 0.4947 31.5072 27.7 91.06 97.96 91.06 90.64 64.35 99.22 72.3 50 0.75947

234 0.2747 22.5646 11.58 95.15 99.08 95.15 92.24 74.56 99.5 88.42 50 0.65432

235 0.9175 35.9841 10.31 88.18 96.89 88.18 89.48 59.18 98.29 89.69 49.99 0.56007

236 1.7449 21.7219 8.95 88.05 98 88.05 93 .79 70.77 98.62 93 .05 50 0.58515

237 0.3952 5.8401 9.02 90.57 99.22 90.57 92.31 86.23 99.5 90.98 50.03 0.3 3706

238 0.3689 5.5379 10.09 90.18 99.08 90.18 92.29 86.15 99.4 89,91 50.01 0.12055

239 0.4081 6.0571 8.64 89.93 99 89.93 92.19 85.51 99.27 91,36 50.01 0.13546

240 1.1084 23.6471 9.22 88.07 97.83 88.07 91 69. Ϊ 8 98.6 90.78 ' 49.99 0.63273 %

% PF % PF Reads % %

% PF Reads Unique % PF Aligned % Strand Target

% % % Off Reads Aligned % PF Reads Unique in Pairs Selected Balance Bases

Chimeras Duplication Bait AP AP Reads Aligned Reads AP Bases AP at l OOX

241 0.515 6.9092 9.31 90.13 98.95 90.13 92.01 84.99 99.31 90,69 50.01 0.14258

242 0.2998 10.6087 8.95 93.93 98.98 93.93 92.17 84.83 99.27 91,05 50.01 0.47302

243 1.7407 26.4448 9 87.84 97.23 87.84 90.68 66.82 98.26 91 ' 49.99 0.58529

244 0.3825 6.7126 8.71 90 99.05 90 92.2 85.03 99.34 91.29 50.01 0.12473

245 0.3739 6.4554 8.72 90.35 99.01 90.35 92.08 85.56 99.3 91.28 50.01 0.15471

246 0.3574 6.2155 8.81 90.01 99.37 90.01 92.26 85.45 99.44 91.19 50.02 0.13404

247 0.3928 6.4002 8.76 90.18 99.08 90.3 8 92.23 85.43 99.37 91.24 50.01 0.13925

248 1 .1297 16.7376 9.59 88.2 99.03 88.2 92.14 74.86 99.27 90.41 50.01 0.53079

249 0.3768 6.0179 10.28 90.42 98.97 90,42 92.19 85.97 99.36 89.72 50.01 0.12352

250 0.7598 13.9336 10.16 88.44 99 88,44 92.02 77.43 99.32 89.84 50 0.49995

251 1 ,4713 39.6237 9.44 87.9 96.02 87,9 88.13 56.16 97.69 90.56 49.98 0.48801

252 0,2142 15.9992 8.78 94.52 ' 99.12 94,52 92.71 ' 80.35 99.44 91.22 50.01 0.54234

253 0.4167 6.2159 8.91 89.85 98.92 89.85 92.1 ' 85.31 99.21 91.09 50.03 0.33805

254 0.5408 60.1975 11.42 90.93 87.17 90.93 66.89 ' 44.2 95.08 88.58 50.03 0.02254

255 2.9456 24.8109 9.84 87.86 96.7 87.86 90.19 68.24 97.71 90.16 50.03 0.51228

256 2.0436 31.0967 9.94 87.33 94.95 87. 1 87.39 63.11 97.34 90.06 49.99 0.54215

257 0.2876 7.944 8.72 90.2 98.9 90.2 93 .92 84.12 99.23 93.28 50.02 0.3 3316

258 0.9606 1 7.8369 8.5 88.56 98.63 88.56 92.17 74.31 99.3 93 ,5 50 0.58999

259 0.3579 4.9697 8.78 90.53 99.27 90.51 92.43 86.94 99.54 93 ,22 50.03 0.3 396

260 0.8587 30.441 8.73 88.18 98.71 88.18 92.43 63.37 99.3 3 93 ,27 50 0.57362

261 0.8965 25.5967 9.01 93.69 98.7 93.69 92.65 71 99.12 90,99 50 0.71782

262 0.5189 4.4414 16.1 98.39 98.73 98.39 91.63 94. Ϊ 5 99.49 83.9 ' 50 0.06802

263 0.4221 5.351 3 9.35 98.57 99.05 98.57 92.12 93.42 99.42 90.65 50 0.08782

264 0.6482 5.518 8.93 98.29 99.34 98.29 92.2 93 99.43 91.07 50 0.08982

265 0.5114 5.3095 10.09 98.54 99.06 98.54 91.86 93.44 99.49 89.91 50.01 0.08611

266 0.4163 5.1947 8.76 98.5 99.28 98.5 92.16 93.49 99.57 91.24 50 0.07893

267 0.4464 5.4382 8.84 98.49 99.28 98.49 92.29 93.26 99.56 91.16 50 0.09768

268 0.467 5.1202 1 1.92 98.51 98.83 98,51 91.92 93.6 99.42 88.08 50 0.07405

269 0.3579 18.1964 9.73 97.02 99.28 97,02 92.61 79.84 99.51 90.27 50 0.74845

270 0,4987 9.5933 7.75 96.16 98.89 96,16 92.81 87.32 99.38 92.25 50 0.42815

271 0,388 8.2638 8.92 96.34 99.27 96,34 92.34 88.69 99.51 91.08 50 0.38682

272 0,41 9.9313 9.06 96.07 ' 99.07 96,07 92.25 * 86.92 99.37 90.94 50 0.43567

273 0.4863 6.8942 9.14 96.25 99.05 96.25 92.03 ' 89.91 99.36 90.86 50 0.27282

274 0.4424 9.1936 9.07 96.28 99.11 96.28 92.23 87.79 99.44 90.93 50 0.40634

275 0.3779 7.961 9.17 96.33 99 96.13 92.02 88.81 99.32 90.83 50 0.32369

276 0.4306 8.4763 8.96 96.32 99.11 96.12 92.08 88.31 99.43 93.04 50 0.39045

277 0.4492 1 8.916 9.56 97.03 99.42 97.03 93.43 79.15 99.6 90.44 50 0.72324

278 0.4034 19.6632 9.47 96.8 99.26 96.8 92.93 78.3 99.47 90.53 50 0.75918

279 0.4756 7.8379 8.96 96.24 99.17 96.24 92.39 89.01 99.48 93 .04 50 0.35862

280 0.4189 7.3346 8.98 96.21 99.24 96.21 92.33 89.45 99.52 91,02 50 0.32538

281 0.3833 19.6474 8.89 97.11 99.07 97.ΪΪ 92.5 78.55 99.44 91.11 ' 50 0.65396

282 3.553 70.2672 1 .13 94.85 86.64 94.85 60.82 37.35 94.75 85.87 49.94 0.00248

283 2.7092 70.6947 13.3 95.3 90.4 95.3 68.24 34.7 95.41 86.7 49.93 0.01224

284 0.2595 11.5547 8.39 96.27 99.39 96.27 92.81 85.57 99.47 91.61 50 0.47617

285 0.2607 12.1296 8.34 96.02 99.3 3 96.02 92.76 84.83 99.43 91.66 50 0.50808

286 9.4725 36.0029 16.95 94.82 89.27 94.82 78.52 64.73 93.19 83.05 49.92 0.1202

287 2.2505 50.6223 10.51 95.58 95.57 95,58 86.26 49.88 97.38 89.49 49.98 0.14866

288 2.2326 74.8428 1 1.8 92.36 95.59 92,36 79.07 26.97 97.41 88.2 49.98 0.19578

289 2.5475 71.9134 12.52 94.62 92.89 94,62 72.72 31.73 96.16 87.48 49.95 0.00587

290 1 ,8887 39.0936 10.7 95.53 94 95,53 84.79 60.96 96.8 89.3 49.98 0.24842

291 1 ,8384 75.9179 11.48 91.97 ' 95.34 91 ,97 77.21 ' 26. ί 97.53 88.52 49.98 0.16162

292 4.5419 75.8174 14.06 92 94.09 92 73.53 ' 26.92 96.39 85.94 49.95 0.3 1693

293 1.8313 42.1142 10.1 95.53 94.72 95.51 85.49 ' 57.98 97.1 89.9 49.98 0.25263

294 0.3696 23.7499 8.52 95.98 97.74 95.98 90.93 74.21 98.9 91.48 50 0.40915

295 0.6945 70.2861 10.16 95.34 95.96 95.34 83 .48 31.48 98.49 89.84 49.98 0.03307

296 0.8858 6.8703 48.65 96.69 97.66 96.69 93 .39 90.35 99.3 53.35 50 0.3 J 083

297 0.8593 4.5684 35.81 98.9 98.19 98.9 93 .58 94.51 99.35 64.19 50 0.09681

298 0.9448 7.8477 42.41 96.92 98.1 96.92 93 .87 89.62 99.43 57.59 50 0.35715

299 0.4112 9.1942 14.87 96.29 98.82 96.29 91.92 87.8 99.38 85, 13 50 0.4538

300 0.4247 9.5012 14.22 96.16 98.81 96.16 91.92 87.41 99.32 85,78 50 0.4664

301 0.489 5.7734 14.63 96.27 99.07 96.27 92.04 90.95 99.51 85,37 ' 50 0.55588 %

% PF % PF Reads % %

% PF Reads Unique % PF Aligned % Strand Target

% % % Off Reads Aligned % PF Reads Unique in Pairs Selected Balance Bases

Chimeras Duplication Bait AP AP Reads Aligned Reads AP Bases AP at 300X

302 0.3943 10.1782 14.43 96.2 98.83 96.2 92.2 86.82 99.36 85,57 50 0.4984

303 0.5248 6.3294 15.23 96.06 98.79 96.06 92.15 90.26 99.29 84,77 50 0.5707

304 0.5978 5.86 15.03 96.17 98.6 96.17 91.83 90.8 99.22 84.97 ' 50 0.50404

305 0.423 9.821 15.74 96.24 98.7 96.24 91.81 87.39 99.36 84.26 50 0.48001

306 0.4373 8.974 14.69 96.1 98.86 96.1 92.1 87.84 99.29 85.31 50 0.42974

307 0.41 27 9.767 14.16 96.12 98.87 96.1 2 92 87.3 3 99.32 85.84 50 0.45123

308 0.3661 10.0921 13.8 96.19 98.97 96.19 92.2 86.87 99.42 86.2 50 0.49146

309 0.3971 5.6833 14.16 96.15 98.94 96.1 5 92.04 90.93 99.37 85.84 50 0.54248 10 0.431 9.8748 1.3.97 96.12 99.02 96.1 92.16 87.03 99.46 86.03 50 0.54569

311 0.3865 6.0955 14.58 96.11 98.92 96.1 1 92.17 90.53 99.38 85.42 50 0.48101

312 0,348 7.4579 15 96.16 98.73 96,16 91.85 89.3 99.35 85 50 0.48206 13 0,3944 10.1848 15.82 96.18 ' 98.63 96,18 91.78 ' 86.8 99.3 84.18 50 0.47833

314 0.5264 9.1835 14.67 96.33 99.08 96.31 92.22 ' 87.8 99.49 85.33 50 0.41376

315 0.4404 10.0205 14.03 96.28 98.92 96.28 92.05 ' 87.01 99.34 85.97 50 0.43376

316 0.4138 11.0639 14.17 96.14 98.95 96.14 92.1 85.92 99.36 85.83 50 0.55819

317 0.5352 6.4623 14 96.04 98.87 96.04 92.11 90.11 99.27 86 50 0.52382

318 0.5125 9.2916 14.25 96.3 98.95 96.3 92.1 87.72 99.39 85.75 50 0.49404

319 0.4762 6.4369 14.47 96.09 98.61 96.09 91 .88 90.19 99.33 85.53 50 0.49449

320 0.4813 6.7067 14.93 96.03 98.71 96.03 91 .8 89.88 99.22 85.07 50 0.55847

321 0.2449 22.5812 13.54 96.16 89.66 96.16 81 .13 77.15 99.22 86.46 50 0.39728

322 0.3354 8.6587 14.07 96.23 98.39 96.23 91.65 88.29 99.35 85,93 50 0.46523

323 0.3624 10.2616 14.46 96.23 98.98 96.23 92.03 86.74 99.45 85,54 ' 50 0.48353

324 0.4239 10.6123 13.75 96.26 98.87 96.26 92.1 86.45 99.35 86.25 50 0.47404

325 0.4227 6.0739 14.22 96.1 98.89 96.1 91.95 90.52 99.29 85.78 50 0.56651

326 0.3928 9.7426 14.09 96.2 98.95 96.2 91.97 87.23 99.4 85.91 50 0.4071

327 0.3723 6.9168 14.47 96.13 98.81 96.1 3 91.99 89.77 99.36 85.53 50 0.5039

328 0.4074 7.8204 14.64 96.27 98.56 96.27 91.81 89.07 99.13 85.36 50 0.50976

329 0.3995 10.2787 15.46 95.99 98.77 95.99 91.9 86.54 99.33 84.54 50 0.47232

330 0.4428 8.7927 14.98 96.1 98.85 96.1 91.9 88.03 99.33 85.02 50 0.42836

331 0,4571 9.9471 14.45 96.13 98.6 96,13 91.67 86.98 99.15 85.55 50 0.46078

332 0,4376 9.1862 14.92 95.99 98.82 95,99 92.12 87.55 99.29 85.08 50 0.46439

333 0,3637 7.5635 14.09 96.07 * 97.2 96,07 90.3 ' 89.23 99.3 85.91 50 0.5795

334 0.489 9.6979 14.65 96.14 98.89 96.14 92.01 ' 87.2 99.34 85.35 50 0.48538

335 0.407 6.9435 14.69 96.2 98.77 96.2 91.98 89.81 99.35 85.31 50 0.51347

336 0.4533 7.634 15.18 96.1 98.84 96.1 92.16 89.07 99.34 84.82 50 0.52386

337 0.561 10.6834 16.4 96.08 98.68 96.08 92.01 86.25 99.29 83.6 50 0.4836

338 0.395 9.3401 14.12 96.31 98.9 96. 1 91 .88 87.68 99.37 85.88 50 0.43754

339 0.3639 9.9809 14.02 96.26 98.92 96.26 91 .99 87.04 99.44 85.98 50 0.46483

340 0.4123 10.3976 14.41 96.28 98.9 96.28 92.14 86.67 99.39 85.59 50 0.53005

341 0.7002 22.1105 16.34 96.23 97.08 96.23 90.34 75.89 98.9 83,66 50 0.47863

342 0.3938 10.9747 14.86 96.1 98.7 96.1 92.12 85.99 99.3 85, 14 ' 50 0.4492

343 0.4586 9.7163 15.19 96.02 98.62 96.02 91.75 87.09 99.26 84.81 50 0.5471

344 0.442 5.9898 15.01 96.14 98.85 96.14 92.18 90.64 99.37 84.99 50 0.53271

345 0.4059 10.4786 15.18 96.06 98.64 96.06 91.78 86.42 99.23 84.82 50 0.48953

346 0.416 9.2908 14.1 1 96.01 98.86 96.01 92.01 87.47 99.33 85.89 50 0.42703

347 0.4375 12.5789 15.04 96.02 98.58 96.02 91.62 84.45 99.18 84.96 50 0.53773

348 0.4532 9.9947 14.41 96.12 98.94 96.1 92.08 86.93 99.4 85.59 50 0.48862

349 0.4418 6.258 14.1 5 96.03 97.76 96.03 91.11 90.36 99.38 85.85 50 0.54278

350 0.4691 11.5633 15.26 96.26 99.03 96.26 92.16 85.54 99.49 84.74 50 0.45872

351 0,4912 7.8277 14.95 96.07 98.47 96,07 91.81 88.9 99.07 85.05 50 0.54974

352 0,3962 8.3244 15.33 96.14 ' 98.72 96,14 91.81 ' 88.48 99.31 84.67 50 0.50426

353 0.4756 9.5712 15.77 96.07 98.67 96.07 91.72 ' 87.28 99.31 84.23 50 0.47479

354 0.40 9.1392 14.37 96.28 98.88 96.28 92.02 ' 87.84 99.36 85.63 50 0.4608

355 0.3997 11.9138 14.31 96.28 98.67 96.28 91.72 85.27 99.21 85.69 50 0.4994

356 0.4544 9.1432 15.54 96.13 98.56 96.13 91 .49 87.74 99.39 84.46 50 0.44317

357 0.4712 5.791 15. 1 96.13 98.86 96.13 92.07 90.82 99.34 84.69 50 0.53393

358 0.4642 1 1.5847 14.93 96.0.3 98.63 96.03 91 .73 85.38 99.39 85.07 50 0.52295

359 0.4008 7.9326 15.1 96.1.3 98.6 96.13 91 .71 88.84 99.39 84.9 50 0.47612

360 0.4609 5.8504 16.15 96.02 98.74 96.02 91.86 90.67 99.27 83,85 50 0.5343

361 0.4421 8.6791 15.83 96.17 98.86 96.17 92.03 88.18 99.37 84, 17 50 0.4726

362 0.4445 8.8396 14.46 96.34 98.81 96.34 91.97 88.18 99.32 85,54 ' 50 0.39545 %

% PF % PF Reads % %

% PF Reads Unique % PF Aligned % Strand Target

% % % Off Reads Aligned % PF Reads Unique in Pairs Selected Balance Bases

Chimeras Duplication Bait AP AP Reads Aligned Reads AP Bases AP at 300X

363 0.4479 10.2878 14.35 96.44 98.8 96.44 91.89 86.91 99.27 85,65 50 0.46698

364 0.486 9.814 15.01 96.16 98.75 96.16 91.66 87.12 99.24 84,99 50 0.45684

365 0.5117 5.5359 14.73 96.15 98.8 96.15 91.97 91.07 99.28 85.27 ' 50 0.51259

366 0.4215 11.9401 15.42 96.1 98.81 96.1 92.06 85.08 99.36 84.58 50 0.51 18

367 0.4753 7.1838 15.33 96.08 98.63 96.08 91.93 89.49 99.16 84.67 50 0.48243

368 0.5776 13.5726 9.73 96.79 98.62 96.79 91.47 84.34 99.19 90.27 49.99 0.37815

369 0.5051 11.4555 9.35 96.63 98.83 96.63 92.09 85.98 99.26 90.65 50 0.36835

370 0.3689 6.8323 9.69 96.87 99.24 96.87 92.34 90.53 99.54 90.31 50 0.23515

37 i 0.3536 7.7226 9.51 96.67 99.05 96.67 92.22 89.5 99.4 90.49 50 0.25722

372 0.3825 9.5468 9.4 96.53 98.83 96.53 91.83 87.69 99.22 90.6 50 0.33491

373 0,3747 6.3652 9.65 96.81 99.03 96,81 92 90.9 99.35 90.35 50 0.18825

374 0,3028 8.5563 9.71 96.67 ' 99.06 96,67 92.18 ' 88.72 99.41 90.29 50 0.24221

375 0.3326 15.3947 9.25 96.53 98.77 96.51 92.23 ' 82.2 99.22 90.75 50 0.41302

376 0.3038 8.647 9.25 96.65 98.97 96.65 92.08 ' 88.62 99.33 90.75 50 0.26195

377 0.3094 9.8061 9.39 96.69 99.11 96.69 92.15 87.55 99.44 90.61 50 0.29098

378 0.3526 7.3309 9.85 96.67 99.02 96.67 93 .89 89.88 99.36 90.15 50 0.20384

379 0.3689 9.3485 9.52 96.64 99.12 96.64 92.13 87.94 99.45 90.48 50 0.2975

3 SO 0.3172 7.5048 9.51 96.65 99.05 96.65 92.11 89.69 99.43 90.49 50 0.23404

381 0.5291 10.3666 9.37 96.97 98.97 96.97 92.54 87.24 99.38 90.63 50 0.27304

382 0.5899 98.3366 72.17 96.3 94.84 96.3 3 5.76 6.33 98.83 27.83 50.03 0

383 0.268 7.66 9.34 96.77 99.16 96.77 92.14 89.64 99.5 90,66 50 0.22179

384 0.3494 8.3225 9.45 96.69 99.03 96.69 91.94 88.96 99.37 90.55 ' 50 0.29295

385 0.2893 9.0533 9.1 1 96.6 99 96.6 92.15 88.2 99.33 90.89 50 0.31456

386 0.3868 8.86 9.43 96.56 98.89 96.56 91.73 88.35 99.24 90.57 50 0.31467

387 0.3557 8.0712 9.46 96.76 99.06 96.76 91.94 89.25 99.4 90.54 50 0.28446

388 0.376 7.8089 9.42 96.68 98.88 96.68 91.66 89.45 99.21 90.58 50 0.29577

389 1 .1 1 72 97.9223 60.43 96.21 94.73 96.21 17.7 6.78 98.34 39.57 50.02 0

390 0.2984 7.7244 9.74 96.69 98.83 96.69 91.64 89.54 99.36 90.26 50 0.27272

391 0.629 12.3053 9.39 96.64 98.27 96.64 91.34 85.24 99.02 90.61 50 0.32459

392 0,3024 8.3113 9.43 96.73 99.1 96,73 92.11 89 99.46 90.57 50 0.27758

393 0,2954 8.8624 9.07 96.73 99 96,73 92.02 88.48 99.35 90.93 50 0.2545

394 0,34 10.1634 9.59 96.56 ' 98.94 96,56 92.07 ' 87.12 99.27 90.41 50.01 0.25285

395 0.3819 7.9704 9.37 96.73 98.98 96.73 91.88 ' 89.32 99.37 90.63 50 0.2081

396 0.3398 9.1602 9.36 96.61 99.02 96.61 91.84 88.1 99.41 90.64 50 0.3236

397 0.4123 8.2766 9.58 96.57 98.86 96.57 93 .63 88.91 99.2.2. 90.42 50 0.282.63

398 0.3716 7.1673 9.61 96.56 98.98 96.56 92.13 89.93 99.36 90.39 50 0.25785

399 0.7631 9.4897 9.32 96.53 98.46 96.51 93 .5 87.75 99.03 90.68 49.99 0.30388

400 0.6749 1 1.4438 9.35 96.6 98.53 96.6 93 .56 86 99.06 90.65 50 0.37667

401 0.6242 12.09 9.31 96.55 98.7 96.55 93 .85 85.33 99.38 90.69 50 0.363 1

402 0.2994 10.1859 9.14 96.59 98.91 96.59 91.88 87.13 99.27 90,86 50 0.31173

403 0.3701 8.2574 9.32 96.6 98.98 96.6 91.93 88.95 99.33 90.68 ' 50 0.28996

404 0.3606 7.3471 9.45 96.78 99.3 1 96.78 92.08 89.94 99.44 90.55 50 0.23407

405 0.2968 9.3624 9.42 96.62 99 96.62 92.02 87.92 99.37 90.58 50 0.28939

406 0.3225 8.2892 9.53 96.61 99.06 96.61 92 88.92 99.4 90.47 50 0.25984

407 0.3998 17.0907 9.04 96.77 98.82 96.77 92.38 80.78 99.28 90.96 50 0.40046

408 0.31 75 7.6473 9.24 96.8 99.37 96.8 92.08 89.68 99.51 90.76 50 0.23397

409 0.3563 8.9565 9.33 96.78 99.32 96.78 92.17 88.43 99.45 90.67 50 0.28136

410 0.3347 8.8451 9.24 96.77 99.06 96.77 91.94 88.52 99.4 90.76 50 0.19546

411 0.3882 7.8705 9.31 96.75 99.06 96.75 91.97 89.44 99.39 90.69 50 0.25188 12 0,2958 7.7213 9.24 96.57 98.88 96,57 91.82 89.42 99.24 90.76 50 0.18231

Ϊ Ϊ3 0,3 12 6.5749 9.6 96.73 ' 99,13 96,73 92.05 ' 90.64 99.44 90.4 50 0.20424

114 0.3386 8.8152 9.56 96.63 98.85 96.61 91.78 ' 88.44 99.24 90.44 50 0.27058

115 0.3045 7.0592 9.38 96.58 99.03 96.58 91.97 ' 90.05 99.37 90.62 50 0.39479

116 0.6231 13.1894 9.38 96.46 98.56 96.46 91.62 84.24 99.06 90.62 49.99 0.40454

417 0.2831 9.8567 8.94 96.63 99.04 96.63 92.16 87.46 99.39 93.06 50 0.26324

418 0.3569 8.6748 9.29 96.63 99.06 96.61 93 .87 88.56 99.4 90.71 50 0.28506

419 0.3859 7.838 9.51 96.76 99.21 96.76 92.27 89.46 99.52 90.49 50 0.22595

420 0.3937 8.0323 9.48 96.6 98.81 96.6 93 .77 89.16 99.36 90.52 50 0.25402

421 0.3699 8.2968 9.53 96.66 99.04 96.66 92 88.96 99.38 90,47 50 0.28684

422 0.3356 6.609 9.78 96.67 99.1 96.67 91.69 90.55 99.43 90,22 50 0.19206

423 0.7576 10.615 9.25 96.69 98.5 96.69 91.7 86.85 99.09 90.75 ' 50 0.30599 %

% PF % PF Reads % %

% PF Reads Unique % PF Aligned % Strand Target

% % % Off Reads Aligned % PF Reads Unique in Pairs Selected Balance Bases

Chimeras Duplication Bait AP AP Reads Aligned Reads AP Bases AP at 300X

424 0.3745 8.9686 9.41 96.72 98.93 96.72 91.96 88.39 99.27 90,59 50 0.28508

425 0.3265 10.3081 9.02 96.72 99.05 96.72 92.19 87.11 99.38 90,98 50 0.29345

426 0.6232 15.0052 9.29 96.5 98.47 96.5 91.59 82.58 99.06 90.71 ' 50 0.39758

427 0.3808 9.1694 9.24 96.51 98.88 96.51 91.75 88.03 99.24 90.76 50 0.25647

428 0.371 i 8.7692 9.42 96.67 98.86 96.67 91.67 88.53 99.22 90.58 50 0.2511 !

429 0.3433 8.1803 9.71 96.52 98.9 96.52 91.74 88.96 99.27 90.29 50 0.26228

430 0.4096 7.4015 9.64 96.71 99.05 96.71 91.86 89.84 99.39 90.36 50 0.25727

43 i 0.3281 6.1683 9.57 96.49 99.05 96.49 91.87 90.8 99.37 90.43 50 0.13913

432 0.3762 9.2883 9.36 96.79 98.91 96.79 91.89 88.34 99.26 90.64 50 0.25913

433 0.3505 8.7448 9.03 96.61 98.93 96.61 91.96 88.5 99.28 90.97 50 0.2512

434 0,3625 7.872 9.29 96.73 99 96,73 92.08 89.42 99.31 90.71 50 0.24334

435 0,3573 9.8956 9.4 96.58 ' 99.06 96,58 92. Ϊ4 * 87.38 99.41 90.6 50 0.32175

436 0.3915 9.2694 9.26 96.59 98.77 96.59 91.7 ' 88 99.13 90.74 50 0.28026

437 0.3241 8.2779 9.38 96.69 99.07 96.69 92.23 ' 89 99.4 90.62 50 0.26226

438 0.3507 7.2517 9.56 96.67 98.99 96.67 92.03 89.95 99.34 90.44 50 0.23885

439 0.337! 7.5052 9.21 96.7 99.12 96.7 92.09 89.73 99.45 90.79 50 0.25574

440 0.3556 8.1136 9.09 96.72 98.89 96.72 93 .74 89.19 99.24 90.91 50 0.23474

44 i 0.3882 8.4055 9.2 96.38 98.97 96.38 93 .92 88.6 99. 3 90.8 50 0.20263

442 0.334 8.4924 9.24 96.73 99.13 96.73 9 ^'^ 88.83 99.46 90.76 50 0.27813

443 0.467 8.9492 9.35 96.79 99.03 96.79 93 .85 88.45 99.38 90.65 50 0.30002

444 0.3992 8.0338 9.29 96.66 98.96 96.66 91.9 89.22 99.28 90,71 50 0.31004

445 0.3843 7.228 9.47 96.72 99.1 96.72 92.14 90.01 99.42 90.53 ' 50 0.21667

446 0.4067 7.8257 9.84 96.75 99.01 96.75 91.97 89.48 99.35 90.16 50 0.24565

447 0.3132 7.5344 9.23 96.69 99.3 1 96.69 92.05 89.69 99.44 90.77 50 0.19563

448 0.6575 11.0072 9.42 96.56 98.39 96.56 91.28 86.38 99 90.58 49.99 0.2728!

449 0.3288 8.7827 9.21 96.55 99.04 96.55 92.2 88.43 99.36 90.79 50 0.28356

450 0.3912 7.4968 9.19 96.71 99.07 96.71 91.9 89.75 99.4 90.81 50 0.2393

45 i 0.414 9.4975 9.41 96.66 99 96.66 91.5 87.83 99.34 90.59 50 0.30262

452 0.4203 7.0882 9.48 96.68 98.92 96.68 91.77 90.32 99.27 90.52 50 0.21204 53 0,4794 8.5432 9. 1 96.6 99.02 96,6 92.06 88.68 99.34 90.49 50 0.33905

454 0,4031 8.5865 9.72 96.63 98.94 96,63 91.93 88.66 99.31 90.28 50 0.27154 55 0,3274 8.3508 9.22 96.64 ' 98.89 96,64 91.74 ' 88.9 99.24 90.78 50 0.26275

456 0.3208 8.9132 9.49 96.59 98.91 96.59 91.71 ' 88.33 99.26 90.51 50 0.25667

457 0.3852 9.2818 9.52 96.72 98.92 96.72 91.95 88.09 99.28 90.48 50 0.27076

458 0.3494 7.9198 9.52 96.7 99.08 96.7 92 89.34 99.4 90.48 50 0.27476

459 0.3649 8.8631 10.03 96.64 98.9 96.64 93 .65 88.42 99.24 89.97 50 0.25804

460 0.3447 9.0461 11.1 96.49 98.82 96.49 93 .8 88.13 99.28 88.9 50 0.3296

46! 0.3203 8.4773 9.49 96.71 99.01 96.71 93 .96 88.84 99.39 90.51 50 0.29948

462 1.1425 25.4646 8.73 93.73 98.06 93.73 93 .8 71.18 98.8 93 .27 49.99 0.69629

463 0.3877 14.4444 9.29 93.96 99.24 93.96 92.22 81.1 99.45 90,71 50 0.69516

464 0.4283 17.3686 9.15 93.84 99.19 93.84 92.33 78.35 99.45 90.85 ' 50 0.68593

465 0.6218 22.0987 9.4 93.96 99.34 93.96 92.63 74.38 99.4 90.6 50 0.73689

466 0.6062 16.5794 9.65 93.62 99.03 93.62 92 78.93 99.3 90.35 50 0.68451

467 0.5935 13.8705 9.44 94.04 99.04 94.04 92.02 81.69 99.3 90.56 50 0.61929

468 0.5563 15.6514 9.4 94.1 99.3 8 94.1 92.27 80.3 3 99.43 90.6 50 0.70032

469 0.4677 15.6764 9.09 93.64 99.07 93.64 92.22 79.75 99.31 90.91 50 0.66497

470 0.7942 17.5966 9.43 93.66 98.93 93.66 92.1 ! 78.06 99.23 90.57 50 0.71072

47 : 0.5472 16.5484 9.34 93.87 99.17 93.87 92.22 79.3.3 99.42 90.66 50 0.70942

472 0.5198 18.2924 9.78 93.85 99.13 93.85 92.12 77.56 99.37 90.22 50 0.6935 !

473 0,6523 16.6944 9.41 93.73 99.11 93,73 92.27 78.91 99.38 90.59 50 0.68582 74 0,5493 15.434 9.42 93.83 ' 99.08 93,83 92.26 * 86.12 99.38 90.58 50 0.64562

475 0.5058 14.8518 9.63 94.04 99.16 94.0 92.38 ' 80.79 99.42 90.37 50 0.66803

476 0.5077 15.2019 9.36 93.93 99.2 93.93 92.31 ' 80.39 99.42 90.64 50 0.70905

477 0.3689 15.4404 9.26 93.88 99.34 93.88 92.44 80.11 99.54 90.74 50 0.5882

478 0.5169 16.5631 9.5 93.88 99.03 93.88 92.28 79.14 99.32 90.5 50 0.63748

479 0.5415 1 8.8112 9.26 93.54 99.05 93.54 92.07 76.84 99.31 90.74 50 0.67386

480 0.634! 20.4685 9.42 93.57 99.03 93.57 92.27 75.39 99.28 90.58 50 0.72529

48! 0.4524 14.4203 9.02 94.07 99.21 94.07 92.39 81.21 99.44 90.98 50 0.62046

482 0.5233 15.3244 9.28 93.9 98.93 93.9 91.99 80.27 99.19 90,72 50 0.60332

483 0.5412 18.754 9.5 93.51 98.97 93.51 92.11 76.89 99.25 90,5 50 0.71107

484 0.5915 15.1233 9.28 93.9 99.06 93.9 92.33 80.45 99.31 90,72 ' 50 0.65572 %

% PF % PF Reads % %

% PF Reads Unique % PF Aligned % Strand Target

% % % Off Reads Aligned % PF Reads Unique in Pairs Selected Balance Bases

Chimeras Duplication Bait AP AP Reads Aligned Reads AP Bases AP at l OOX

485 0.4491 14.2668 9.39 94.02 99.07 94.02 91.88 81.31 99.36 90,61 50 0.53509

486 0.4206 19.6526 9.46 93.75 99.15 93.75 92.21 76.24 99.41 90.54 50 0.68078

487 0.1774 98.8265 10.15 93.34 90.97 93.34 8,17 9.36 99.13 89,85 49.99 6.00E- 05

488 0.437 1 8.1539 8.95 93.61 98.97 93.61 93 .76 77.51 99.24 93 ,05 50 0.65844

489 0.372 18.6829 9.28 93.94 99.21 93.94 92.39 77.25 99.46 90,72 50 0.70176

490 0.3624 18.0511 9.13 93.74 99.15 93.74 92.24 77.66 99.41 90,87 50 0.65637

49 ϊ 0.3716 22.1999 9.38 94.09 98.94 94.09 92.2 74.17 99.22 90.62 ' 50 0.65162

492 0.4663 20.5451 9.39 93.63 99.34 93.63 92.41 75.32 99.4 90.61 50 0.72635

493 0.3618 16.4907 9.29 93.6 99.07 93.6 92.13 78.97 99.32 90.71 50 0.6337

494 0.369 19.1387 9.28 93.87 99.04 93.87 91.99 76.8 99.26 90.72 50 0.68852

495 0.4517 22.2378 9.47 93.49 99.04 93.49 92.09 73.72 99.31 90.53 50 0.6794

496 0.4147 17.3303 8.05 93.23 98.97 93.23 91.89 77.96 99.27 91.95 50 0.59947

497 0.4276 19.8996 9.34 93.74 99.33 93,74 92.31 76.03 99.36 90.66 50 0.70608

498 0.4063 14.506 9.24 93.98 99.37 93,98 92.23 81.05 99.42 90.76 50 0.61867

499 0,4361 15.9174 9.32 93.45 99.08 93,45 92.2 79.38 99.36 90.68 50 0.67061

500 0,3616 20.9931 9.37 93.73 ' 99.19 93,73 92.38 ' 74.99 99.43 90.63 50 0.73045

501 0,3635 20.3584 9.39 94.04 ' 99.13 94.04 92.43 ' 75.8 99.4 90.61 50 0.69047

502 0.3311 15.1191 9.25 94.07 99.21 94.07 92.24 ' 80.56 99.47 90.75 50 0.52805

503 0.3745 18.2889 9.11 93.86 99.15 93.86 92.15 77.55 99.43 90.89 50 0.63349

504 0.4191 10.7957 9.03 89.54 99.08 89.54 92.18 81.02 99.31 90.97 50 0.49107

505 0.523 10.3382 8.99 89.58 99.04 89.58 92.19 81.41 99.27 91.01 50 0.423 24

506 0.5402 1 1.6614 9.15 89.88 99.18 89.88 92.2 80.49 99.43 90,85 50 0.38366

507 0.4273 10.8951 8.91 89.35 99.19 89.35 92.43 80.77 99.4 93 ,09 50 0.42501

508 1.11 1 .7345 8.91 89.53 98.67 89.53 93 .89 79.33 98.98 93 ,09 50 0.44399

509 0.4831 10.5527 8.85 89.57 98.85 89.57 91.93 81.22 99.1 91, 15 50 0.36681

510 0.6112 12.3596 8.99 89.91 98.97 89.9Ϊ 91.79 79.98 99.25 91.01 ' 50 0.48021

511 0.3961 11.0526 8.82 89.35 98.83 89.35 91.8 80.63 99.09 91.18 50 0.43635

512 0.4067 11.1381 8.73 89.2 98.91 89.2 91.85 80.45 99.14 91.27 50 0.42144

513 0.3535 11.7653 8.82 89.5 99.32 89.5 92.16 80.33 99.34 91.18 50 0.40645

514 0.4467 10.5727 8.87 89.54 99.04 89.54 91.96 83.39 99.27 91.13 50 0.42068

515 0.41 89 10.9229 8.84 89.39 99.09 89.39 92.2 80.77 99.33 91.16 50 0.4381

516 0,3944 10.2864 8.66 89.36 99.36 89,36 92.34 81.28 99.37 91.34 50 0.41353

517 0,4759 12.377 8.48 89.53 98.84 89,53 92 79.67 99.18 91.52 50 0.4263

518 0,3205 12.9135 8.71 89.64 99.05 89,64 91.94 79.28 99.3 91.29 50 0.4349

519 0,5753 14.7431 8.25 89.37 98.42 89,37 91.39 77.58 99.01 91.75 50 0.46895

520 0,4758 13.5681^" 8.86 89.69 ' 98.97 89,69 91.99 ^" 78.77 99.22 91.14 50 0.4701

521 0.4762 12.6001 8.79 89.33 98.91 89.33 91.78 ' 79.31 99.13 91.21 50 0.47254

522 0.4974 12.5351 8.87 89.36 98.82 89.36 91.93 79.37 99.06 91.13 50 0.43124

523 0.5327 10.6934 8.67 89.74 99.15 89.74 92.07 81.23 99.36 91.33 50 0.379

524 0.6293 14.6085 8.26 89.39 98.47 89.39 91 .6 77.72 98.9 93.74 50 0.49386

525 1.0424 1 7.7109 9.88 87.85 98.53 87.85 92.13 74.02 98.82 90.12 50 0.38716

526 0.3897 10.7617 8.49 89.39 99.02 89.39 92.01 80.93 99.26 93 ,51 50 0.4259

527 0.631 33.9673 9.91 88.2 96.99 88.2 88.31 60.92 98.4 90,09 50 0.40446

528 0.4932 15.2057 8.61 89.14 98.83 89.14 92.03 77.02 99.18 91,39 50 0.50838

529 0.4481 15.2395 8.56 89.17 98.96 89.17 91.96 77.01 99.22 91.44 50 0.47346

530 0.6739 17.9776 7.9 89.51 97.94 89.5Ϊ 91.46 74.99 98.65 92, Ϊ ' 49.99 0. 1982

531 0.4152 10.8733 8.48 89.69 99.05 89.69 92.21 81 99.3 91.52 50 0.33332

532 0.614 16.6851 8.4 88.99 98.87 88.99 92.15 75.7 99.22 91.6 50 0.52811

533 2.0752 46.1706 12.35 89.67 88.93 89.67 75.05 54.07 94.68 87.65 49.99 0.27462

534 0.4856 13.6593 8.82 89.07 98.94 89.07 91.9 78.26 99.23 91.18 50 0.47383

535 0,3411 11.9253 8.71 89.03 98.89 89,03 91.8 79.65 99.14 91.29 50 0.38137

536 0,4051 11.7694 8.51 89.36 98.93 89,36 91.95 80.04 99.1 91.49 50.01 0.38826

537 0,3654 33.2771 8 88.86 98.72 88,86 92.07 61.32 99.09 92 50 0.37352

538 0,4223 12.6218 8.53 89.46 98.8 89,46 92.1 79.34 99.03 91.47 50 0.38046

539 0,6428 26.3337 11.74 97.23 ' 99.28 97,23 92.86 ' 72.23 99.5 88.26 50.01 0.66515

540 0.5235 23.5802 9.81 97.5 99.19 97.5 92.91 ' 75.06 99.41 90.19 50.03 0.74946

541 0.9471 26.1364 10.07 97.58 99.29 97.58 93.66 ' 72.56 99.55 89.93 50.03 0.61957

542 0.4996 12.0073 10.46 97.55 99.28 97.55 92.51 86.14 99.53 89.54 50.03 0.38423

543 0.2812 63.3633 10.97 97.15 98.92 97.15 91 .02 36.7 99.36 89.03 50.03 0.25668

544 0.7804 1 5.3872 8.68 96.33 99.08 96.33 92.32 82.03 99.32 91.32 50 0.60432

%

% PF % PF Reads % %

% PF Reads Unique % PF Aligned % Strand Target

% % % Off Reads Aligned % PF Reads Unique in Pairs Selected Balance Bases

Chimeras Duplication Bait AP AP Reads Aligned Reads AP Bases AP at l OOX

667 0.3857 38.7653 11.66 95.92 95.22 95.92 86.07 61.22 99.51 88.34 50 A

668 0.4641 38.5181 12.07 95.82 94.43 95.82 85.01 61.65 99.29 87,93 50 A

669 0.5554 62.4577 12.17 95.84 95.84 95.84 83.71 39.15 99.53 87.83 ' 50 NA

670 0.5063 37.7601 12.04 95.79 94.95 95.79 85.8 62.35 99.45 87.96 50 NA

67 i 0.4364 42.9237 12.6 95.64 93.46 95.64 82.5 57.97 99.07 87.4 50 NA

672 0.4103 43.4764 13.8 96.04 94.9 96.04 83.98 57.09 99.39 86.2 50 NA

673 0.3316 45.1 13 J 12.19 95.75 94.45 95.75 83.95 55.68 99.35 87.83 50 NA

674 0.3367 40.2532 12.06 95.97 95.51 95.97 86.46 59.79 99.56 87.94 50 NA

675 0.3899 36.0348 1 3.54 95.75 94.79 95.75 85.64 63.72 99.38 88.46 50 NA

676 0.5336 36.5476 1 1.75 95.9 95.23 95.9 86.32 63.39 99.36 88.25 50 NA

677 0,5 40.4836 11.02 95.79 95.21 95,79 85.84 59.57 99.32 88.98 50 0.16248

678 0,496 44.0342 10.55 95.45 ' 94.12 95,45 83.84 ' 56.63 99.07 89.45 50 NA

679 0.354 42.6454 11.53 95.87 94.66 95.87 84.64 ' 57.92 99.53 88.47 50 NA

680 0.4227 39.1891 11.61 95.88 95.21 95.88 86.12 ' 60.8 99.54 88.39 50 NA

681 0.493 37.2525 11.99 96.08 95.38 96.08 86.27 62.62 99.62 88.01 50 NA

682 0.6775 42.3775 11.62 95.3 94.3 95.3 83.91 57.94 99.1 1 88.38 49.99 NA

683 0.2788 39.6945 12.1 96.03 95.56 96.03 86.5 60.28 99.55 87.9 50 NA

684 0.4557 39.2102 11.1 95.96 95.45 95.96 86.53 60.73 99.42 88,81 50 NA.

685 0.4983 9.6499 9.68 91.3 98.73 91.3 91 .79 83.17 99.23 90,32 50 0.57052

686 0.5666 1 1.8238 9.74 90.73 98.92 90.73 92.22 80.83 99.35 90,26 50 0.70377

687 0.5443 10.7777 10.23 90.93 98.86 90.93 91.71 81.9 99.3 89,77 50 0.68191

688 0.5327 11.4402 14.95 91.06 98.89 91.06 92.12 81.43 99.4 85.05 ' 50 0.67989

689 0.4962 12.1281 9.51 90.92 98.71 90.92 92.02 80.75 99.13 90.49 50 0.67613

690 0.6051 9.2458 9.59 91.04 98.79 93.04 91.84 83.3 99.22 90.41 50 0.54602

69 i 0.4897 11.9139 9.64 91.06 98.88 93.06 92.03 83.03 99.32 90.36 50 0.6909

692 0.5917 12.5637 10.64 90.99 98.78 90.99 91.98 80.43 99.26 89.36 50 0.64664

693 0.5198 12. S776 10.05 91.23 98.89 93 .23 92.21 80.95 99.36 89.95 50 0.62326

694 0.5754 12.2538 9.59 90.94 98.96 90.94 92.3 80.64 99.36 90.41 50 0.63737

695 0.5475 11.0739 9.79 90.92 98.96 90.92 92.15 83.62 99.38 90.21 50 0.65332

696 0,5217 12.2615 9.53 90.96 98.95 90,96 92.35 80.64 99.37 90.47 50 0.667

697 0,4795 13.6455 9.59 90.92 98.93 90,92 92.31 79.43 99.35 90.41 50 0.68292

698 0,5261 9.4402 9.68 91.17 ' 98.84 91 ,17 91.67 ' 83.25 99.29 90.32 50 0.50717

699 0.5948 12.4573 9.49 91.36 98.87 91.36 91.89 ' 80.8 99.33 90.51 50 0.63371

700 0.5875 9.431 9.94 91.35 98.98 91.15 92.15 83.22 99.41 90.06 50 0.52392

70S 0.2249 37.0653 13.48 91.94 98.75 91.94 90.92 59.76 99.28 86.52. 50 NA

702 0.3772 34.3096 13 93.39 99.04 91.19 91 .19 61.69 99.32 87 49.99 NA

703 0.4178 27.8447 11.99 93.34 98.92 91.14 91 .41 67.36 99.2 88.01 50 0

704 0.2863 71.3245 14.48 88.3 96.06 88.1 80.3 29.4 98.32 85,52 49.97 NA.

705 0.3246 38.7411 13.14 88.84 98.75 88.84 90.98 56.77 99.05 86,86 49.99 NA.

706 0.3147 56.8688 13.65 88.57 94.65 88.57 80.76 42.8 97.83 86,35 49.96 NA

707 0.1783 85.845 17.9 87.38 92.6 87.38 1.44 18.53 97.67 82, Ϊ ' 49.96 NA

708 0.3532 69.2639 15.02 87.95 93.3 87.95 68.9 33.86 96.73 84.98 49.95 NA

709 0.66 58.9982 34.55 88.56 94.34 88.56 79.79 43.2 97.42 85.45 49.95 NA

710 0.4126 71.5931 34.05 88.36 96.3 88.36 80.12 29.33 98.22 85.95 49.98 NA

711 0.4471 93.5574 33.65 88.86 98.83 88.86 73.35 6.84 99.25 86.35 49.99 NA

712 0.3832 62.5821 32.22. 88.39 97.28 88.39 86.43 36.46 98.67 87.78 49.98 NA

713 0.5402 46.6817 12.48 88.17 98.57 88.1 7 90.29 49.59 99.11 87.52 50 NA

714 0.4355 27.6033 12.65 89.39 99.06 89.39 91.16 66.49 99.34 87.35 50 NA

715 0.289 31.5476 10.75 89.69 99.25 89.69 91.84 63.27 99.48 89.25 50 NA

716 0,3938 30.3977 13.3 88.97 98.99 88,97 91.19 63.87 99.29 86.7 50 NA

717 0,4103 33.7459 12.61 88.48 ' 98,89 88,48 91.24 ' 60.75 99.18 87.39 49.99 NA

718 0.3584 28.4441 13.29 89.35 99.01 89.35 91.46 ' 65.78 99.23 86.71 50 NA

719 0.3526 33.8375 12.4 89.45 99.12 89.45 91.39 ' 61.19 99.36 87.6 50 NA

720 0.6768 45.9574 12 88.58 98.35 88.58 89.74 50.55 98.97 88 49.98 NA

72 S 0.3867 35.4693 12.34 88.43 98.87 88.43 90.97 59.28 99.17 87.66 49.99 NA

722 0.4247 34.8686 12.43 88.79 99.03 88.79 91 .2.4 59.94 99.34 87.57 50 NA

723 0.5418 8.8334 12.42 94.56 98.42 94.56 91 .58 86.71 99.3 87,58 50 0.50599

724 0.4919 1 2.2722 12.96 94.23 98.91 94.21 91 .91 83.28 99.38 87,04 50 0.61 194

725 0.5072 9.1249 24.01 94.42 98.31 94.42 91.58 86.32 99.17 75,99 50 0.53534

726 0.5119 7.1747 38.74 94.28 98.04 94.28 91.52 87.96 99.27 61,26 50 0.47392

727 0.5274 8.7275 14.39 94.36 98.74 94.36 91.98 86.6Ϊ 99.2 85.61 ' 50 0.59996 %

% PF % PF Reads % %

% PF Reads Unique % PF Aligned % Strand Target

% % % Off Reads Aligned % PF Reads Unique in Pairs Selected Balance Bases

Chimeras Duplication Bait AP AP Reads Aligned Reads AP Bases AP ai l OOX

728 0.5156 7.8018 14.25 94.25 98.53 94.25 91.61 87.36 99.12 85,75 50 0,42802

729 0.4644 10.9334 12.97 94.53 98.86 94.53 91.8 84.76 99.37 87,03 50 0,62285

730 0.4873 9.1588 30.59 94.14 98.18 94.14 91.52 86.05 99, 15 69,41 ' 50 0,52224

73 i 0.4287 7.4145 33.77 94.44 98.27 94.44 91.84 87.88 99.31 68.23 50 0.44892

732 0.542 12.2863 12.09 94.35 98.95 94.35 92.09 83.38 99.4 87.91 50 0.63945

733 0.41 81 8.7823 30.51 94.23 98.02 94.23 91.42 86.49 99.3 69.49 50 0.51562

734 0.4645 9.9694 19.37 94.16 98.74 94.16 92.28 85.32 99.36 80.63 50 0.62384

735 2.5568 9.4608 16.1 2 93.77 96.5 93.77 89.69 85.6 98.09 83.88 49.99 0.41775

736 0.461 7.3056 19.1 1 94.39 98.53 94.39 91.66 87.92 99.33 80.89 50 0.40822

737 0.4736 9.7928 1 1.1 94.53 99 94,53 92.12 85.79 99.44 88.9 50 0.57997

738 0,525 8.3832 37.71 94.21 97.9 94,21 91.2 86.82 99.27 62.29 50 0.46646

739 0,4255 10.1437 24.45 94.07 ' 98.14 94,07 91.53 ' 85.13 99.12 75.55 50 0.57337

740 0.4688 8.9423 40.87 94.07 97.49 94.07 90.95 ' 86.23 98.98 59.13 50 0.51373

741 0.4617 10.8588 20.07 94.62 98.75 94.62 92.18 ' 84.9 99.38 79.93 50 0.57664

742 0.4 15 11.3174 10.97 94.38 98.89 94.38 92.09 84.28 99.27 89.04 50 0.64991

743 0.48 10.8259 12.05 94.03 98.71 94.03 91 .82 84.45 99.18 87.95 50 0.621 59

744 0.4307 8.5531 11.08 94.22 99.12 94.22 92.13 86.62 99.47 88.92 50 0.53531

745 0.4427 7.4646 21.73 94.25 97.92 94.25 90.98 87.7 99.2 78.27 50 0.41681

746 0.505 1 .9383 11.75 94.42 98.89 94.42 92.01 82.84 99.34 88.25 50 0.64894

747 0.4039 1 1.3233 13.85 94.33 98.8 94.33 92.01 84.25 99.35 86.15 50 0.59204

748 0.4819 9.4313 27.99 93.89 97.89 93.89 91.16 85.63 98.92 72,01 50 0,56319

749 0.5318 7.9692 32.61 94.43 98.25 94.43 91.97 87.37 99,21 67.39 ' 50 0,47011

750 0.4426 8.9013 23.93 94.29 98.28 94.29 91.67 86.42 99.12 76.07 50 0.54928

75 i 0.3926 8.1613 1 3 94.24 99.02 94.24 92.24 87.03 99.41 89 50 0.50374

752 0.6481 11.3951 15.52 94.16 98.56 94.16 91.66 84.05 99.22 84.48 50 0.53671

753 0.51 39 8.8759 19.34 94.4 98.63 94.4 91.9 86.52 99.41 80.66 50 0.44439

754 0.5143 11.2658 22.63 94.03 97.95 94.03 90.89 84.3 1 99.05 77.37 50 0.51651

755 0.4867 8.75 10.94 94.45 98.92 94,45 92 86.65 99.35 89.06 50 0.42335

756 0.6221 12.5673 12 94.22 98.44 94,22 91.57 83.06 98.97 88 50.01 0.59977

757 0,448 7.3779 28.53 93.99 98.19 93,99 91.35 87.51 99.19 71.47 50 0.42843

758 0,4607 10.4202 17.85 94.07 98.65 94,07 91.82 84.85 99.34 82.15 50 0.59212

759 0,5248 8. Ϊ31 16.6 94.17 ' 98.5 94,17 91.56 ' 86.3 99.11 83.4 50 0.52556

760 0.5419 11.216 11.8 94.63 98.87 94.61 92.13 ' 84.57 99.29 88.2 50 0.56105

761 0.5168 11.7644 11.17 94.44 98.88 94.4 92.05 83.92 99.3 88.83 50 0.56737

762 0.628 1 3.5253 12.09 94.39 98.64 94.39 91 .91 82.32 99.17 87.91 50 0.6079

763 0.5168 8.8762 31.34 93.91 97.88 93.91 91 .44 86.14 99.06 68.66 50 0.49901

764 0.6457 8.3487 25.34 94.33 98 94.33 91 .45 86.96 98.96 74.66 50 0.39699

765 0.4884 8.9038 11.81 94.38 98.76 94.38 92.02 86.47 99.23 88.19 50 0.49456

766 0.6375 9.1325 14.73 94.18 98.44 94.18 91 .22 86.1 99.16 85.27 50 0.41662

767 0.6611 11.8399 10.86 94.28 98.97 94.28 92.02 83.71 99.38 89, 14 50 0,58403

768 0.6108 12.4774 12.09 94.26 98.86 94.26 92.06 83.14 99,31 87,91 ' 50 0,58878

769 0.5511 12.9759 12.27 94.55 98.86 94.55 92.18 82.92 99.3 87.73 50 0.60165

770 0.5811 12.2889 1 3.17 94.31 98.83 94.31 91.99 83.35 99.26 88.83 50 0.57776

77 i 0.6096 11.803 1 3.77 94.17 98.72 94.17 91.95 83.69 99.22 88.23 50 0.60956

772 0.4681 9.7516 10.91 94.45 99.3 2 94.45 92.33 85.75 99.5 89.09 50 0.57673

773 0.4504 8.0924 24.44 94.27 98.55 94.27 91.63 87.1 1 99.35 75.56 50 0.453

774 0.5941 10.4416 22.35 94.21 98.26 94,21 91.48 84.97 99.16 77.65 50 0.53476

775 0.3812 7.9522 10.83 94.25 99.02 94,25 92.12 87.2 99.39 89.17 50 0.52801

776 0.5627 9.8752 10.55 94.51 98.91 94,51 91.81 85.68 99.31 89.45 50 0.50372

777 0,533 12.5354 11.48 94.15 98.81 94,15 91.99 83 99.27 88.52 50 0.61067

778 0,5923 8.4753 40.76 94.06 ' 97.45 94,06 90.88 ' 86.61 99.13 59.24 50 0.39078

779 0.6094 12.0942 14.01 94.12 98.7 94.12 91.84 ' 83.38 99.23 85.99 50 0.56987

780 0.6027 11.3254 11.55 94.1 3 98.7 94.11 91.82 ' 84.07 99.13 88.45 50 0.59756

781 0.5203 7.4723 33. 1 94.1 3 97.89 94.11 91.52 87.56 98.98 66.59 50 0.5028

782 0.5824 7.7132 36.22 93.99 97.79 93.99 91 .1 8 87.23 99.06 63.78 50.01 0.43044

783 0.6494 8.0165 23.02 94.08 98.03 94.08 91 .43 87.05 99.25 76.98 50 0.41514

784 0.695 9.714 11.48 94.53 98.73 94.51 91 .71 85.85 99.21 88.52 50 0.39597

785 0.4566 9.8268 13.67 94.25 98.71 94.25 91 .82 85.53 99.24 86.33 50 0.47823

786 0.5459 11.3534 11.16 94.4 99.01 94.4 92.29 84.26 99,44 88,84 50 0,59486

787 0.5771 11.0745 10.81 94.22 98.89 94.22 92.07 84.38 99,32 89, 19 50 0,58144

788 0.4848 12.802 12.52 94.36 98.93 94.36 92.12 82.83 99.34 87,48 ' 50 0,54375 %

% PF % PF Reads % %

% PF Reads Unique % PF Aligned % Strand Target

% % % Off Reads Aligned % PF Reads Unique in Pairs Selected Balance Bases

Chimeras Duplication Bait AP AP Reads Aligned Reads AP Bases AP at l OOX

789 0.5121 9.0783 22.97 94.29 97.97 94.29 91.25 86.28 99.24 77,03 50 0.45912

790 0.4846 10.8302 10.43 94.58 99.01 94.58 92.25 84.88 99.38 89,57 50 0.57111

79 ϊ 0.5422 10.8082 11.07 94.37 98.92 94.37 92.08 84.73 99.35 88.93 ' 50 0.48994

792 0.5168 15.4539 1 3.07 94.68 98.67 94.68 91.75 80.72 99.07 88.93 50 0.60214

793 0.5587 9.0913 12.54 94.39 98.67 94.39 91.88 86.27 99.25 87.46 50 0.46 74

794 0.437 8.0128 12.4 94.41 99.04 94.41 92.29 87.29 99.42 87.6 50 0.55448

795 0.31 85 98.5862 13.67 93.54 74.75 93.54 3.08 24.5 98.99 86.33 50.01 1.00E- 05

796 0.0968 96.5293 17.21 93.46 78 93.46 9.64 23.05 99.35 82.79 50 0

797 0.104 98.11 32 13.08 92.12 39.82 92.12 0.91 56.02 98.69 86.92 50.02 2.00E- 05

798 0.1106 98.7007 13.48 93.63 79.84 93.63 3,88 19.76 99.26 86,52 50 Ϊ.00Ε- 05

799 0.1165 95.7494 12.32 91.03 17.06 91.03 0,65 76.05 97.62 87,68 50.03 Ϊ .00Ε- 05

800 0.1447 96.1854 11.93 91.98 32.28 91.98 3.47 63.32 98.51 88.07 49.99 4.00E- 05

801 0,3927 13.5219 12.73 95.03 ' 98.73 95,03 92.02 ' 82.82 99.23 87.27 50 NA

802 0.364 11.5555 11.99 95 98.94 95 92.25 ' 84.58 99.39 88.01 50 NA

803 0.5405 31.2066 10.44 94.54 98.43 94.54 91.74 ' 66.31 98.99 89.56 50 NA

804 0.3361 10.9463 10.1 95.03 98.7 95.01 91.82 85.15 99.07 89.9 50 NA

805 0.9302 95.7754 20.1 93.98 85.48 93.98 34.6 16.81 95.48 79.9 50 NA

806 0.9574 96.11 11 17.79 93.93 84.87 93.93 33.34 17.07 94.69 82.22 50.02 NA

807 0.3204 10.5335 10.44 95.09 98.97 95.09 92.32 85.59 99.34 89.56 50 NA.

808 4.631 72.4723 34.91 93.83 85.71 93.83 54.74 35.71 93.86 65.09 50.03 NA.

809 1.6386 91.1638 14.61 94.27 94.44 94.27 54.93 13.16 97.72 85.39 49.99 NA.

810 0.2542 14.5925 9.84 95.04 99.07 95.04 92.69 81.81 99.39 90, 16 50 NA

811 0.2543 14.5213 10.02 95.17 98.91 95.17 92.57 82 99.31 89.98 ' 50 NA

812 0.2372 16.3658 9.5 95.04 99.03 95.04 92.63 80.38 99.38 90.5 50 NA

813 0.3064 13.2694 10.89 95.03 99.08 95.03 93 83 99.45 89.11 50 NA

814 3.497 89.7189 16.38 94.39 93.97 94.39 56.33 14.85 96.89 83.62 49.96 NA

815 0.3501 11.9667 12.8 94.7 98.63 94.7 92.03 83.99 99.1 87.2 50 NA

816 5.5259 86.6657 27.71 93.07 85.39 93.07 37.52. 24.23 93.78 72.29 49.98 NA

817 1 .0566 96.7873 14.72 94.5 88.36 94,5 15.63 13.74 97.16 85.28 49.99 NA

818 0.4254 5.1443 48.29 92.38 97 92,38 90.63 88.07 99.16 51.71 50 NA

819 0,9992 9.8861 46.07 92.49 95.52 92,49 88.51 84.2 98.36 53.93 49.99 NA

820 0,3847 5.0062 49.31 93.16 97.85 93,16 91.63 88.86 99.09 50.69 50 NA

821 1 ,0034 8.2212 48.88 92.71 ' 95, 12 92,71 88.11 ' 85.82 98.26 51.12 50 NA

822 0.1786 18.0951 33.49 92.82 97.76 92.82 90.97 ' 77.13 99.18 66.51 49.99 NA

823 0.3114 8.265 24.01 92.98 98.2 92.98 91.54 85.87 99.18 75.99 49.99 NA

824 0.2256 14.3784 18.37 93.16 98.77 93.16 92.08 80.6 99.45 83.63 50 NA

825 0.5143 4.9035 54.74 92.87 97.41 92.87 93 .07 88.67 98.96 45.7.6 50 0

826 0.4766 5.758 50.63 93.53 97.52 93.51 93 .21 88.53 99.34 49.37 50 NA

827 0.3854 6.9273 38.02 93.1 98.33 93.1 93 .88 87.12 99.33 63 .98 50 NA.

828 0.2679 6.5659 51.9 92.79 97.32 92.79 93 .44 87.19 99.2 48.1 50 NA.

829 0.3332 6.005 43.75 92.95 98.17 92.95 91.75 87.78 99.33 56,25 50 NA

830 0.4451 7.7235 34.93 92.79 98.26 92.79 91.7 86. Ϊ 5 99.2 65,07 ' 50 NA

831 0.38 6.1834 35.72 93.5 98.26 93.5 91.62 88.33 99.27 64.28 50 NA

832 0.7227 17.2068 12.37 93.17 98.04 93.17 91.31 78.39 98.99 87.63 49.99 NA

833 0.1927 7.1396 52.78 92.66 97.74 92.66 92 86.56 99.28 47.22 50 NA

834 0.3903 6.1931 48.2 92.51 95.6 92.51 89.28 87.35 98.95 51.8 50 NA

835 0.2888 7.2923 53.34 92.79 97.43 92.79 91.09 86.55 99.04 48.66 50 NA

836 0,8196 10.7443 40.69 93.07 96.24 93.07 89.12 83.9 98.57 59.31 49.99 NA

837 0,3676 8.5488 19.41 93.18 98.76 93.3 8 91.88 85.76 99.32 80.59 50 NA

838 0,2085 11.5374 28.36 92.57 98.2 92.57 91.64 82.66 99.22 71.84 50 NA

839 0,3521 11.7382 16,34 92.93 98.98 92,93 92.02 82.7 99.4 83.66 50 NA

840 1 ,0148 6.1061 50.07 93.14 ' 95.07 93,14 88.3 ' 88 98.34 49.93 50 NA

841 0.2459 10.042 38.14 92.99 97.96 92.99 91.61 ' 84.31 99.27 61.86 50 NA

842 0.3743 6.1227 43.46 93.07 97.9 93.07 91.74 87.81 99.22 56.54 50 NA

843 0.381 1 5.9932 49.18 92.56 97.33 92.56 90.96 87.47 98.8 50.82. 50 NA

844 0.2752 5.9564 43.38 93.05 85 93.05 78.37 88.59 99 56.62. 50 NA %

% PF % PF Reads % %

% PF Reads Unique % PF Aligned % Strand Target

% % % Off Reads Aligned % PF Reads Unique in Pairs Selected Balance Bases

Chimeras Duplication Bait AP AP Reads Aligned Reads AP Bases AP ai l OOX

845 0.3993 7.571 39.97 93.01 97.75 93.01 91.45 86.5 98.99 60,03 50 A

846 0.5 9.2866 12.16 93.09 97.82 93.09 91.27 85.12 99.34 87,84 50 A

847 0.435 5.272 47.39 92.72 94.52 92.72 88.41 88.36 99.05 52,61 ' 50 NA

848 3.1873 9.4943 45.35 92.59 93.62 92.59 85.82 84.74 97.88 54.65 50 NA

849 0.3018 6.3109 46.99 92.59 97.54 92.59 91.18 87.22 99.06 53.01 50 NA

850 0.3703 6.839 24.1 8 93.21 98.56 93.21 91.91 87.3 99.35 75.82 50 NA

85 i 0.3918 8.283 31.63 92.93 98.1 5 92.93 91.55 85.8 99.03 68.37 50 NA

852 0.6144 7.6186 39.94 92.65 97.03 92.65 90.86 86.38 98.84 60.06 49.99 NA

853 0.4674 15.0422 32.77 9'? ¾ ¾ 96.48 92,33 90.22 79.6 98.8 67.23 49.99 NA

854 0.1936 10.1402 45.93 93.08 96.84 93,08 90.52 84.38 99.13 54.07 50 NA

855 0,1311 45.6025 41.49 92.76 89.89 92,76 78.99 55.68 99.29 58.51 50.01 NA

856 0,1495 40.7299 42.45 92.82 * 92.29 92,82 83.28 ' 58.89 99.23 57.55 50.01 NA

857 0.1535 48.5054 53.84 9Ϊ.99 88.73 91.99 75.96 ' 53.37 99.01 46.16 50.03 0.32985

858 0.2272 29.9624 48.46 92.99 94.77 92.99 87.18 ' 67.42 98.9 51.54 50.03 0.25996

859 0.2406 40.9221 36.82 91.78 95.59 91.78 87.94 57.07 99.17 63.18 50 NA

860 0.6528 1 5.9144 10.72 92.86 98.61 92.86 92.28 79.01 99.38 89.28 49.99 NA

86 S 0.0995 98.272 27.88 91.03 64.93 91.03 2.24 32.79 98.52 72.12 50.02. NA

862 0.363 33.0005 51.93 93.45 95.06 93.45 87.54 64.97 99.04 48,07 50 NA.

863 0.2815 16.6765 9.84 93.68 99.33 93.68 92.55 78.82 99.55 90, 16 50 NA.

864 0.3815 16.3386 10.03 93.6 99.37 93.6 92.5 79.08 99.58 89,97 50 NA.

865 0.3493 20.8057 9.6 94.07 99.3 94.07 92.96 75.4 99.55 90,4 50 NA

866 0.3345 16.5943 9.98 93.5 99.19 93.5 92.5 78.8 99.4 90,02 ' 50 NA

867 0.2344 16.1752 9.69 93.58 99.38 93.58 92.63 79.24 99.39 90.31 50 NA

Max

GSSR PF ID of Insert HQ Mean

Estimated Fold 80 XX Size Error Mean Insert Library Base Fo!d Picard Genome STD library Max insert Rate Bait Size Size Penalty Enrichment Data Size INS Size IIS Size INS AL Coverage INS

6! 42489904 3.86 40.47 351401 3101976562 41.83 28486062 248760407 3 .04 43.14 347.79

62 136221065 2.49 53.27 336441 3101976562 43.84 119959559 236433631 0.18 104.27 357.96

63 163866166 2.61 54.14 336444 3101976562 42.82 145103028 240043 125 0.18 116.05 153 .48

64 225283771 2.55 52.28 336439 3101976562 49.49 198969673 246028454 0.18 99.78 169.85

65 224796856 17.5 53.35 336442 3101976562 47.81 198727853 247814664 0.23 113.42 163.15

66 180985306 20.41 54.21 336445 3101976562 _t 46.87 159870881 246578281 0.26 111.84 1 4.64

67 240999180 2.69 54.26 336448 3101976562 _t 45.71 2Ϊ4226970 ' 238532743 0.18 Ϊ 20.29 152.52

68 252455337 2.69 54,34 336451 3103976562 46.16 225086672 248759947 0.18 Ϊ22.6 153.9

69 224437341 2.65 53.92 336456 3103976562 45.43 199575520 236757690 0.18 106.18 156.46

70 231994058 2.64 53.98 336459 3303976562 47.79 205983391 244457075 0.18 1 30.54 155.19

71 67766555 3.3 2 57.79 336443 3303976562 31.53 59698882 248759938 0.24 1 3 3 .89 120.82

72 59149853 2.33 53.89 330250 3303976562 56.99 53281764 248759948 0.19 73.4 166.65

73 519387679 2.42 27.6 346310 3103976562 62.38 232513435 247052340 0.2 81.5 169.39

74 367550520 2.44 34.3 3 346311 3103976562 79.52 199745888 243082055 0.19 47.78 186.58

75 440192506 2.42 30.64 346312 3101976562 64,53 207237096 242600566 0.19 88.25 179.55

76 241675015 2.49 ' 50.35 353911 ' 3101976562 68.4 210044483 248759942 0.8 ' 134,98 179.71

77 223380435 2.66 ' 49.83 353923 ' 3101976562 67.85 193857511 248760511 0.8 ' 136,48 182.6

78 225918368 2.42 50.63 353947 3101976562 61.97 195281539 248760161 0.8 ' Ϊ37.77 173.23

79 209362220 2.69 50.07 353969 3101976562 68.65 181198899 248774447 0.79 127.76 179.81

80 240771196 2.57 49.97 353889 3101976562 72.02 208650459 233936568 0.8 120.1 382.76

8! 240009085 2.62 50.85 353901 3101976562 62.86 209200953 248759951 0.8 141.71 373.26

82 221175135 2.39 50.57 353912 3101976562 69.93 192189775 242072001 0.79 136.17 177.63

83 204246567 2.6 51.46 353924 3101976562 61.29 178238424 242555682 0.79 128.33 173 .32

84 21 8658713 2.47 50.36 353936 3101976562 65.79 187881396 242555684 0.79 126.63 174.52

85 229724630 2.46 50.29 353970 3101976562 _t 69.29 198873901 239858860 0.79 128.6 176.93

86 224601899 2.41 50.37 353902 3101976562 _t 67.36 194993903 ' 242555683 0.79 Ϊ 32.94 178.64

87 207486052 2.41 50.7 353913 3103976562 64.23 179878147 240721394 0.82 ϊ 23.64 174.95

88 197262438 2.49 50.66 353925 3103976562 71.77 170667169 245780636 0.82 127.46 177.99

89 214522573 2.45 50.47 353891 3103976562 65.2 186525851 248759949 0.8 132.63 177.76

90 228099597 2.58 50.54 353903 3303976562 72.04 398250212 248759950 0.83 125.26 179.67

91 197978674 2.65 49.46 353914 3303976562 79.56 370997065 243082779 0.83 108.68 186.93

92 219997006 2.52 50.62 353926 3103976562 69.56 193061127 238423641 0.8 11 .47 177.95

93 202885235 2.46 50.5 353950 3103976562 68.55 175962430 242550971 0.79 123.84 177.85

94 218906598 2.45 50.61 353961 3101976562 67.14 190125891 248759949 0.79 134,72 176.16

95 213308150 2.46 50.45 353972 3101976562 68.34 184320329 237458687 0.81 119,42 175.84

96 238142727 2.49 ' 49.94 353892 ' 3101976562 67.73 206884825 248759949 0.8 * 123,25 182.07

97 225022001 2.61 50.72 353904 3101976562 63.78 194651303 248760475 0.79 ' Π9.Ϊ5 171.81

98 395761789 2.57 52.63 353915 3101976562 59.03 170781336 248759949 0.81 126.47 160

99 3 80342958 2.64 51.61 353927 3101976562 _, 65.3 156774573 248760746 132.48 369.88

100 23 2700386 2.47 51.07 353939 3101976562 61.63 185011826 245763 249 0.79 138.64 373 .66

101 23 2774300 2.46 51.4 353951 3101976562 59.63 185322970 248760204 0.79 130.49 369.45

102 3 56985597 3.02 55.06 353962 3101976562 40.36 136872937 248759948 0.82 155.77 135.74

103 232107864 2.51 49.29 353893 3101976562 73.5 201450043 244796536 0.8 110.17 188.87

104 201391856 2.47 51.56 353905 3101976562 61.47 174953929 242551553 0.79 133.31 167.63

105 251906480 2.42 49.66 353928 3101976562 _t 73.6 219683505 247718891 0.79 124.22 186.41

106 227165877 2.72 52.99 353940 3101976562 _t 54.91 200696214 ' 248760497 0.8 Ϊ 34.23 158.02

107 203593558 2.47 51.59 353952 3103976562 61.29 176921205 248760200 0.81 128.87 166.81

108 197053 386 2.42 50.99 353963 3103976562 65.37 170707016 248760189 0.79 223.77 170.58

109 215933936 2.42 49.59 353973 3303976562 74.07 386932284 245296728 0.8 122.25 185.51

1 10 196163305 2.45 50.55 353894 3303976562 64.83 370395027 246373895 0.83 1 34.2 178.33

1 11 209994436 2.53 50.99 353906 3103976562 65.15 182531124 243083352 0.8 129,74 172.99

1 12 206428539 2.69 50.38 353929 3103976562 69.67 178695281 248759943 0.79 112.46 176.73

1 13 193669378 2.48 50.63 353941 3103976562 72.47 167805415 236464172 0.79 106,2 176.95

114 196277382 2.47 51.47 353964 3101976562 65.57 170427789 248759949 0.8 126,64 167.47

115 211845685 2.48 ' 51.33 353974 ' 3101976562 61.7 183 19003 248759949 0.8 ' 134,32 168.35

116 204946415 2.44 50.65 353895 3101976562 61.73 178124037 248759949 0.79 ' Ϊ3 Ϊ.92 174.92

117 385901785 2.44 49.76 353907 3101976562 78.28 159937536 248760512 0.8 ' ϊί ί. Ϊ 183.75

118 395356154 2.43 51.11 353918 3101976562 63.19 169312336 236308036 0.81 138.09 171.67

119 23 1339417 2.48 50.94 353930 3101976562 68.86 183823296 244752400 0.8 129.71 373.33

120 393831019 2.44 51.18 353942 3101976562 63.39 168366354 248759947 0.8 127.08 373 .61

Max

GSSR PF ID of Insert HQ Mean

Estimated Fold 80 XX Size Error Mean Insert Library Base Fo!d Picard Genome S D library Max insert Rate Bait Size Size Penalty Enrichment Data Size INS Size IIS Size INS AL Coverage INS

30 S 537574616 2.5 49.29 332047 3101976562 56.96 435991439 243369805 3 .4 123.63 356.03

302 270242982 2.43 49.27 332056 3101976562 61.3 217781644 242555678 3 .4 111.09 356.61

303 519261094 2.43 48.38 332065 3101976562 61.7 413068983 248759938 3 .4 126.72 163 .78

304 495701371 2.48 49.3 332074 3101976562 55.48 393325403 247053088 3 .39 113.17 153.71

305 282794006 2.52 48.57 332082 3101976562 57.96 224919981 248760019 1.4 110.21 155.64

306 281867695 2.4 47.74 332021 3101976562 _t 60.81 226994370 244950391 1.41 98.32 171.1

307 265072673 2.5 48.69 332030 3101976562 _t 63.53 214630801^" ' 248760397 1.4 102.85 164.08

308 269474835 2.46 49.4 332039 3103976562 58.06 239772913 247547889 1.4 110.22 159.25

309 539603386 2.5 49.51 332048 3103976562 56.3 438911164 246145727 1.39 120.8 156.55

310 301261235 2.55 49.78 332057 3103976562 54.46 247688228 248759947 1.39 123 .37 154.5

311 447143534 2.46 49.3 3 332066 3103976562 58.22 358303437 248760520 1.4 107.73 157.83

312 364431337 2.49 49.45 332075 3103976562 58.14 287940196 237477154 1.4 108.84 151.41

313 268234081 2.45 48.23 332083 3103976562 59.42 232399222 248759942 1.4 107.47 158.37

314 268795529 2.49 47.88 332022 3103976562 59.76 235956740 239436740 1.41 97.49 169.24

315 251319909 2.46 47.89 332031 3101976562 66.25 203959577 248759948 1.4 98.7 173.12

316 280853936 2.48 ' 49.25 332040 ' 3101976562 59.75 229297265 248759949 1.4 * 124,88 158.45

317 461380163 2.45 ' 48.98 332049 ' 3101976562 59.16 373501012 246787970 1.4 ' 116,4 163.38

318 295993052 2.48 49.23 332058 3101976562 58.16 242492842 248760495 1.39 ' 110.73 158.59

319 443398726 2.48 49.35 332067 3101976562 58.9 3549471 36 246330867 1.4 111.02 156.52

320 478505151 2.51 48.68 332076 3101976562 61.48 381786656 245686438 3 .4 123.88 359.92

321 102751759 2.47 49.76 332084 3101976562 55.67 84547544 248759940 3 .39 92.4 355.33

322 298260984 2.44 49.45 332023 3101976562 60.88 242837476 248759950 3 .4 104.28 157.4

323 264760545 2.54 48.84 332032 3101976562 63.03 215529832 248760419 3 .4 108.9 163 .04

324 247382520 2.44 49.67 332041 3101976562 57.45 201494577 248759948 3 .4 106.82 157.23

325 539027096 2.55 49.37 332050 3101976562 _t 56.38 437443065 245675298 1.39 127.93 158.98

326 243126001 2.49 48.98 332059 3101976562 65.27 198ΪΪ3806 ' 248759940 1.4 95. i i 162.45

327 409669275 2.47 49.2 332068 3103976562 63.66 327108864 248760471 1.4 Ϊ 12.6 157.63

328 369192654 2.45 49.33 332077 3103976562 59.89 294291750 248759948 1.4 Ϊ 13.9 155.01

329 261674775 2.48 48.4 332085 3103976562 62.62 208517494 248759944 1.4 106.26 158.59

330 291753052 2.53 48.33 332024 3103976562 64.41 235209690 248759943 1.43 100.46 165.45

331 265820161 2.48 48.72 332033 3103976562 63.63 235316872 248759940 1.4 104.09 162.52

332 287791519 2.53 48.92 332042 3103976562 57.83 232294853 248759950 1.39 105.31 157.45

333 429378691 2.56 50.27 332051 3103976562 51.06 350777354 236304324 1.39 130,99 149.65

334 2805798 1 2.56 49.39 332060 3101976562 54.99 228693898 248759946 1.39 109,64 154.24

335 412732732 2.52 49.72 332069 3101976562 55.71 329257168 246092820 1.4 115,07 151.3

336 386383351 2.45 ' 48.64 332078 ' 3101976562 57.69 304282548 248302263 1.4 ' 116.33 158.99

337 257254050 2.47 48.14 332086 3101976562 59.34 202033387 248759950 1.4 ' Ϊ08.Ϊ8 155.53

338 274866137 2.62 48.78 332025 3101976562 63.53 224271374 245497886 1.4 102.28 163.99

339 262174029 2.59 49.52 332034 3101976562 59.82 213870446 246963383 _r_ E 9__→ 106.31 356.57

340 271857114 2.5 49.3 332043 3101976562 59.3 3 221371233 248759951 3 .4 114.33 356.53

341 131231101 3.66 51.1 332052 3101976562 42.66 100041209 248759958 3 .37 117.71 322.19

342 230681878 2.51 49.59 332061 3101976562 54.68 185216947 245606528 3 .4 102.78 153 .49

343 31 3175450 2.48 49.53 332070 3101976562 56.48 246708629 248759939 3 .4 122.14 149.84

344 501231490 2.52 49.64 332079 3101976562 53.42 399897638 244896549 1.39 119.63 149.85

345 263885384 2.51 48.92 332087 3101976562 _t 58.01 211173629 246750234 1.4 109.85 155.38

346 265851634 2.47 49.05 332026 3101976562 63.35 2Ϊ6437878 ' 248760385 1.4 98.81 161.21

347 239277269 2.51 49.02 332035 3103976562 59.53 193787351 243951982 1.4 119.54 155.13

348 273138376 2.58 49.51 332044 3103976562 55.59 222937165 248760447 1.4 110.65 154.44

349 486707386 2.56 49.72 332053 3103976562 55.31 395404684 248760385 1.39 123 .68 154.55

350 224428642 2.48 48.6 332062 3103976562 59.43 379598874 242430123 1.4 104 158.37

351 400734095 2.5 49.49 332071 3103976562 55.73 339243165 248759944 1.4 123,33 152.36

352 349802392 2.57 48.78 332080 3103976562 59.61 276399368 248759945 1.4 115,04 156.52

353 282885319 2.56 48.62 332088 3103976562 57.8 226742782 248759940 1.39 107,08 155.04

354 285902994 2.43 48.82 332027 3101976562 62.03 231947010 248759943 1.4 104,25 161.94

355 236671309 2.52 ' 49.26 332036 ' 3101976562 61.86 192275689 248760450 1.4 ' 112.88 157.45

356 284917105 2.7 48.44 332045 3101976562 59.26 2293711 32 245953733 1.39 ' Ϊ02.94 160.05

357 536601787 2.59 48.65 332054 3101976562 60.49 428627643 248759947 1.39 ' Ϊ20.32 158.06

358 253190572 2.51 49.15 332063 3101976562 57.72 204029203 248759950 1.4 116.94 155.07

359 345366285 2.45 48.81 332072 3101976562 61.97 272544803 248759944 3 .4 107.35 358.05

360 537248073 2.51 47.93 332081 3101976562 60.32 424708380 248760215 3 .39 119.12 360.22

Mean Median Min Number

Read Mean Insert insert of SNPs On Bait

Length target Size Size Near Bait in Off Bait On Bait vs On Target

AP ('overage INS INS Bases dbSNP Bases Bases Selected Bases

76 161.38 154 2 1421347540 NA 880285608 6740495297 0.83 5249286853

76 149.09 364 2 1490323232 NA 880683658 6239693026 0.83 4855400925

76 149.31 332 2 939046384 NA 3096605944 6175681523 0.87 4863774253

76 144.26 358 2 1345497772 NA 926534919 6033498373 0.82 4696385603

76 141.01 168 1516207537 NA 802674467 5906554972 0.8 4594419104

76 130.73 164 2 1316765333 NA 734994171 5469749287 0.83 4256968165

76 139.17 166 2 1432900095 NA 786336462 5825060769 0.8 4533790772

76 ΪΪ5.46 167 2 1236056140 ' NA 682328243 4835814064 0.8 3760124300

76 135.9 167 2 3395658865 NA 785796334 5685364171 0.8 4427764588

76 122.87 167 3 3269625853 NA 696616373 53 2534529 0.8 4000364600

76 147.41 132 2 924814737 NA 865659260 6325276174 0.87 4800865950

76 141.36 162 2 3430424515 NA 790103093 5937885315 0.81 4604470739

76 1 15.62 162 3 3 323 294023 NA 660264872 4833931523 0.81 3762389465

76 144.56 164 4 1447012150 NA 857150959 6027031931 0.81 470793 5830

76 1 34.76 158 2 1268010614 NA 752343997 56363 75888 0.82 4387939993

76 1 53.06 140 2 1 309063548 NA 797425759 6352285327 0.85 4981232040

76 145.45 144 2 1062206650 NA 805539349 5992297390 0.85 4736435976

76 142.55 138 2 989636071 NA 792380394 * 5923349708 0.86 4641454807

76 142.62 173 2 1545675471 NA 825241944 ' 5966609774 0.79 4643802753

76 125.53 63 2 1259272541 NA 684213165 ' 5251095492 0.81 4088432985

76 146.39 353 2 1313487402 NA 807600518 6128161330 0.82 4773567350

76 141.9 368 2 145681 3587 NA 832281504 5915393677 0.8 4619462868

76 125.84 364 2 1255700826 NA 723 3 10160 5238285339 0.83 4095983277

76 123.24 169 2 1301216793 NA 705354063 5159066039 0.8 4011111567

76 128.58 169 2 1353216782 NA 7593 78984 5350932898 0.8 4184408930

76 128.31 162 2 1235626347 NA 695762038 5358599667 0.81 4177348550

76 132.43 164 3 1318052460 NA 724956647 5528949045 0.81 4312370961

76 126.18 165 2 1266Ϊ98653 ' NA 686458655 5279669032 0.81 107865968

76 163.43 128 2 940581975 NA 822532792 676754Ϊί92 0.88 5322202196

76 158.35 135 2 3 305491358 NA 807328279 6604275917 0.86 5154390536

76 1 29.46 136 2 907242684 NA 690708440 5385866297 0.86 4212426510

76 1 35.7 167 2 3405450856 NA 752498560 5680828654 0.8 4420326972

76 J 47.22 139 2 3059782080 NA 735996740 6344330344 0.85 4792766850

76 149.88 131 2 953339678 NA 675961984 6235217414 0.87 4877529382

76 140.38 135 2 939332408 NA 858892437 5830933434 0.86 4571572521

76 161.44 138 2 1064622631 NA 833750128 6711 11429 0.86 5257050701

76 135.38 159 2 1301460725 NA 743203808 ' 5673091016 0.81 4414929770

76 148.32 335 2 1005918032 NA 786055441 ' 6174691705 0.86 4821789339

76 178.09 336 2 1160016533 NA 859314380 ' 7421212727 0.86 5798045323

76 150.26 325 2 867751635 NA 688268322 6264257893 0.88 4889011317

76 143.23 333 2 925085779 NA 734930404 5966090862 0.87 4663706719

76 139.79 333 2 928111482 NA 693040242 5825425342 0.86 4550378192

76 152.56 124 2 872619689 NA 759477058 6344982436 0.88 4965271254

76 134.36 158 2 1276697788 NA 723399116 5620515235 0.83 4375726936

76 123.95 167 2 1275666347 NA 703072211 5180867287 0.8 4035270587

76 125.65 166 2 1300265823 NA 722981899 5247067744 0.8 4090039134

76 128.78 160 2 1260067480 ' NA 719010325 5385606293 0.81 193963468

76 130.13 159 2 3271087586 NA 747047050 5443028361 0.81 4237408783

76 117.83 168 2 3262329950 NA 652828070 4930698264 0.8 3836236416

76 125.08 162 2 3265391705 NA 683186234 5233584116 0.81 4074056282

76 i 26.99 162 2 3259406424 NA 682085374 5332318114 0.81 4134922066

76 3 27.01 168 2 3368321567 NA 707837566 5339336119 0.8 4136949686

76 3 28.24 165 2 1324259748 NA 704306684 5364391569 0.8 4175383796

76 3 28.89 121 2 733249967 NA 757999534 5400632100 0.88 4195585508

76 149.73 131 2 988 11872 NA 697970783 6263580622 0.86 4872115559

76 142.68 145 2 1135071522 NA 794001433 5955491989 0.84 4643014251

76 149.21 135 2 1045400862 NA 689086456 * 6247065671 0.86 4156599804

76 127.39 338 3 958373443 NA 540800098 ' 5342056453 0.85 4135919902

76 91.03 354 2 850518053 NA 3047518769 3790402883 0.82 2957635840

76 122.93 333 2 76759352.7 NA 639497900 5103148037 0.87 4000156030

76 46.35 343 2 401951327 NA 968645092 1935720058 0.83 3490733099

76 112.24 354 2 911499323 NA 482089253 4678427346 0.84 3648123457

Mean Median Min Number

Read Mean Insert insert of SNPs On Bait

Length target Size Size Near Bait in Off Bait On Bait vs On Target

AP ('overage INS INS Bases dbSNP Bases Bases Selected Bases7 76 161.72 153 2 1457497446 NA 830153739 6808819724 0.82 52708150338 76 133.69 152 2 1 1785893 33 NA 695075578 5617772536 0.83 43566109669 76 122.45 156 2 1 153482428 NA 658773240 5136168288 0.82 39897931240 76 265.19 149 2 2330553337 NA 3470836274 11 11884553 2 0.83 86467171981 76 149.06 155 2 1389511433 NA 836548760 6246264476 0.82 48522342232 76 126.51 157 2 1191126853 NA 658790547 5312012358 0.82 41210423263 76 150.37 154 2 1389683912 NA 805061377 6306358463 0.82 49011328954 76 142.94 152 2 12907)85552 ' NA 781720305 599747⁾5805 0.82 46598005165 76 144.03 153 2 1294747103 NA 764760956 604703Ϊ886 0.82 46943035886 76 136.15 154 2 1251568857 NA 731599285 5709395715 0.82 44375304727 76 240.19 156 2 2358080955 NA 1405784024 10081952798 0.81 78293243898 76 1 39.7 155 2 3300966785 NA 929649699 5848568484 0.82 45455591279 76 142.22 161 2 3428320914 NA 752787578 5962613781 0.81 462883 84960 76 1 54.18 153 2 1399202856 NA 813745806 6462530964 0.82 5024360982 ϊ 76 145.68 153 2 1338337803 NA 862144908 6102683896 0.82 47430468392 76 1 51.76 151 2 1317770801 NA 786814392 6347240800 0.83 49406959593 76 148.93 149 2 1284908222 NA 756317260 6258386637 0.83 48541716404 76 153.06 153 2 1394487773 NA 837548591 ' 6413385821 0.82 4 188950655 76 134.99 150 2 1155328931 NA 750032750 ' 5652Ϊ33580 0.83 439207 1076 76 128.99 158 4 1262540852 NA 692731144 ' 5403252528 0.81 41984142807 76 144.43 158 2 1385999343 NA 783961244 6051194175 0.81 47015897728 76 150.47 150 2 1288526269 NA 774314372 6301660843 0.83 48980972649 76 137.92 157 2 1350045326 NA 785010223 5791894385 0.83 44959440560 76 95.68 152 2 866542799 NA 523580834 4013131577 0.82 31156742051 76 140.35 151 1286423727 NA 785326922 5895496702 0.82 45762005172 76 138.25 145 2 1161003236 NA 1048096051 5786441738 0.83 45027545453 76 135.41 154 3 1269610199 NA 69 121608 5693727578 0.82 44062132774 76 144 154 2 1321756241^" ' NA 762469663 6032615407 0.82 46875084605 76 141.56 151 2 1254481836 NA 716118405 5939634503 0.83 46083582616 76 146.02 151 2 1323320894 NA 771091282 61 35308546 0.82 47545781657 76 148.32 154 2 3360456886 NA 776669344 6236438711 0.82 48335485588 76 145.6 151 2 3299126453 NA 960329830 63 3 3012820 0.82 47452844119 76 142.53 146 3 3200570375 NA 862329653 5984060579 0.83 46443420440 76 80.17 155 2 753278754 NA 428736803 3363 3 51058 0.82 2608683959 ϊ 76 65.23 147 3 552342189 NA 333606423 2738368136 0.83 21214840892 76 143.15 154 2 1325989025 NA 768636382 6003795234 0.82 46595618723 76 129.18 149 2 1106053363 NA 659337369 ' 54289Ϊ6389 0.83 42085257074 76 128.75 152 3 1165077642 NA 683379832 ' 5417748382 0.82 41944196105 76 118.72 1 9 2 1097131223 NA 1299711352 ' 4978222638 0.82 38685978506 76 226.75 153 2 2163206003 NA 2830917990 9520441442 0.81 73923467437 76 153.24 155 2 1442153433 NA 903418600 6425372908 0.82 49908534548 76 129.45 159 2 1282639521 NA 732896553 5443375973 0.83 42184894689 76 138.57 156 2 1333927736 NA 750515572 5815729175 0.83 45148036690 76 158.99 150 3 1378683583 NA 833347295 6668632255 0.83 51815461941 76 144.69 153 2 1286795103 NA 781987468 6074121544 0.83 47095576252 76 126.83 154 2 1190376739 NA 697551293 5320252757 0.82 1314896993 76 2Ϊ6.0Ί 149 2 2 Ϊ 82306447 ' NA 4318600706 908827⁾Ϊ059 0.81 70494301594 76 159.36 147 2 1372355514 NA 1054631450 6677298640 0.83 51902627215 76 143.2 116 2 686411251 NA 763373600 5954037884 0.9 46603335926 76 146.47 136 2 1033647406 NA 706839730 6157034546 0.86 47707382917 76 54.17 165 2 538073026 NA 275237230 2257065269 0.81 17586670558 76 55.53 165 2 540749304 NA 321166008 2320363998 0.81 18030788449 76 57.81 164 6 554305883 NA 280878555 2435908107 0.81 18779432710 76 1 57.15 127 2 933925329 NA 757459244 6544217984 0.88 51149586221 76 59 150 2 486938752 NA 302890674 2462608607 0.83 19164313072 76 116.54 153 3 951492598 NA 571574845 4860038308 0.84 37910761203 76 151.69 125 2 883273963 NA 715 Ϊ 89633 ' 6344496834 0.88 49412241434 76 55.53 160 2 507245857 NA 269071097 ' 2312378488 0.82 18036393805 76 60.65 157 3 526213536 NA 293924234 2529511508 0.83 19708912436 76 57.64 365 2 560080094 NA 286771536 2406392230 0.83 3 8730999177 76 57.84 360 2 528273090 NA 282285568 2410282562 0.82 3 8797699508 76 123.56 356 3 1 138244500 NA 668658710 5165738958 0.82 4022707953

Mean Median Min Number

Read Mean insert insert of SNPs On Bait

Length target Size Size Near Bait in Off Bait On Bait vs On Target

AP ('overage INS INS Bases dbSNP Bases Bases Selected Bases

311 76 115.58 1 7 2 979167306 NA 993810891 4833098730 0.83 3766254909

312 76 116.95 140 3 918925926 NA 3024358416 4883859995 0.84 3808720280

313 76 115.16 147 1 996729821 NA 3093267303 4822353363 0.83 3752528174

314 76 104.68 159 7 1015025732 NA 926577288 4374231837 0.81 3406150588

315 76 105.66 160 2 1067754138 NA 897064269 4428519464 0.83 3442999544

316 76 133.99 1 7 2 1147348403 NA 3 3 34125593 5603569557 0.83 4363983487

317 76 125.07 153 2 1116828488 NA ^■031897359 5223055332 0.82 407345193 Ϊ

318 76 Π8.9Ϊ 148 2 10 4751690 ' NA 993957449 4968560762 0.83 3870955373

319 76 119.26 145 3 986688770 NA 1009923596 4983448137 0.83 3882739715

320 76 132.88 148 3 1 357198176 NA 1178287351 5558559494 0.83 4331 322069

321 76 98.96 145 2 833996052 NA 779579330 4146059520 0.83 3219947276

322 76 1 12.04 146 2 942702522 NA 920214758 4678959263 0.83 3646463386

323 76 1 16.92 148 2 3030248682 NA 1000370258 4886409429 0.83 3809677150

324 76 1 14.63 147 2 963 360383 NA 917348329 4792939296 0.83 3732086522

325 76 1 37.66 149 2 3 354753968 NA 1142654335 5740456148 0.83 4483337237

326 76 102.23 149 2 9073 14938 NA 848515866 4267433031 0.82 3328235734

327 76 120.94 145 2 ^■019672264 NA 1027318798 5052479873 0.83 3937490707

328 76 122.28 143 2 ^■003230569 NA 1048888502 ' 5 i 10693100 0.84 3982065550

329 76 113.92 1 6 2 989533839 NA 1052571232 ' 4768035083 0.83 3712065402

330 76 107.92 153 2 996958963 NA 970038469 ' 4507861072 0.82 3511759151

331 76 111.64 150 3 999365869 NA 957544995 4670488765 0.82 3637682893

332 76 113.08 147 7 955319839 NA 996418787 4725392704 0.83 3680712507

333 76 140.78 140 7 1066550830 NA 3 339276014 5877624697 0.85 4581982838

334 76 117.77 1 4 2 957667323 NA 3008485454 4919374228 0.84 3832798302

335 76 123.7 141 961512468 NA 3054497968 5163137092 0.84 4027949923

336 76 124.94 148 2 1072936405 NA ^■ 126133086 5219584477 0.83 4067963524

337 76 116.21 144 2 973674919 NA ^■ 143274542 4854197410 0.83 3782851876

338 76 109.86 152 2 995889508 ' NA 918546501 45892697 Ϊ 0.82 3575554056

339 76 113.79 145 2 955901479 NA 933751633 4770377672 0.83 3708358150

340 76 122.54 145 2 1027318105 NA 1036598068 5130240872 0.83 3993821838

341 76 1 28.01 113 3 696470612 NA 1167253423 5283685798 0.88 4164430484

342 76 1 10.56 141 2 863 873272 NA 955208105 463 3 887677 0.84 3598439450

343 76 1 31.27 138 2 3007555496 NA 1161994376 5480629631 0.84 4276008514

344 76 1 8.69 140 i 985307183 NA 1121923606 5367807668 0.84 4188397956

345 76 1 17.74 145 4 978999848 NA 1057146252 4929096106 0.83 3836348739

346 76 106.06 149 2 933183768 NA 881572749 4433627907 0.83 345 Ϊ 767807

347 76 128.16 143 2 ^■063295258 NA 1 Ϊ38Ϊ29235 ' 5364009683 0.83 4178190853

348 76 118.58 1 4 2 968238472 NA 999158920 ' 4964866023 0.84 3863708670

349 76 130.78 1 4 2 1056983360 NA 1074501834 ' 54596534-33 0.84 4257096761

350 76 111.62 1 7 2 958277965 NA 1032647188 4666351063 0.83 3633500604

351 76 132.6 142 2 1040966789 NA 1 356004735 5533912909 0.84 4317939159

352 76 123.57 145 2 1031866203 NA 3 323 540885 5161725059 0.83 4025110694

353 76 115 1 4 949408274 NA 3077308160 4804639985 0.84 3745668433

354 76 H i.94 150 2 994075335 NA 9523 26507 4677721677 0.82 3643560179

355 76 121.33 145 2 1025503428 NA 3036967791 5064832509 0.83 3948169857

356 76 110.58 150 2 948773558 NA ^■024044687 4618927075 0.83 3602101007

357 76 12 .29 146 2 1098966821 ' NA ^■ 174407349 5398683676 0.83 4210249600

358 76 125.45 144 2 1031281572 NA 1101599445 5247003353 0.84 4089356955

359 76 115.33 146 2 975656448 NA 1030220820 4836856807 0.83 3755927972

360 76 127.88 149 2 1 3 39578415 NA 1244974732 5345039762 0.83 168083724

361 76 1 14.63 151 2 3027445041 NA 109426693 1 4790803008 0.82 3730275373

362 76 100.59 156 2 949468301 NA 871359663 4204646366 0.82 3273333326

363 76 1 13.58 150 2 3009032606 NA 965535379 4753364278 0.82 3703529062

364 76 1 11.88 150 2 9883 35980 NA 1000602838 46763 28314 0.83 3642733771

365 76 122.92 152 2 ^■096551907 NA 1077404607 5139115497 0.82 4007467455

366 76 122.86 146 2 ^■049249965 NA 1127314425 5134900848 0.83 40010871 1

367 76 116.33 151 3 ^■050832557 NA 1070750104 ' 4863236257 0.82 3787610014

368 76 97.84 139 2 694598190 NA 534160416 ' 4075797632 0.85 3180330097

369 76 95.4 1 6 2 763693560 NA 490501078 3989456028 0.84 3105355500

370 76 74.97 171 4 795450707 NA 423407434 3130165028 0.8 2437596080

371 76 78.14 169 2 816258249 NA 429468798 3268208838 0.8 2543564938

372 76 90.5 158 2 821535662 NA 477473098 3781994320 0.82 2947506683 Mean Median Min Number

Read Mean Insert insert of SNPs On Bait

Length target Size Size Near Bait in Off Bait On Bait vs On Target

AP ('overage INS INS Bases dbSNP Bases Bases Selected Bases

373 76 67.5 166 2 677812397 NA 373072638 2814595235 0.81 2194690696

374 76 75.91 161 3 752061523 NA 423423202 3167163435 0.83 2468353679

375 76 102.71 130 2 661960857 NA 503952482 4280369883 0.87 3333782445

376 76 79.3 162 3 767831527 NA 436412751 3317049806 0.83 2579043218

377 76 83.69 159 2 772603786 NA 443818361 3491073604 0.82 2721740541

378 76 70.08 169 2 74262431 1 NA 400561031 2922097058 0.8 2278436627

379 76 84.51 166 2 838774944 NA 459174129 3525741612 0.81 2748286680

380 76 71.52 161 3 6911022.77 ' NA 386419605 29870Ϊ2784 0.81 2327289735

381 76 80.25 169 3 696349725 NA 416097757 3328754061 0.83 2608749146

382 76 0.56 146 4 2770587 NA 30214773 8883860 0.76 6908856

383 76 72.92 160 2 698516493 NA 386062029 3050233624 0.81 2370599167

384 76 84.07 160 2 789030191 NA 448432609 3509537129 0.82 2734353548

385 76 87.37 162 2 845362107 NA 451756585 3663390933 0.81 2845653 784

386 76 87.48 161 6 820219306 NA 465248630 36503 84746 0.82 2846333957

387 76 82.68 161 5 777356850 NA 441671293 3449737957 0.82 2689556892

388 76 84.13 154 2 738060418 NA 441952457 3532301181 0.83 2738745235

389 76 0.83 159 8 4702756 NA 34096274 17623727 0.79 13696176

390 76 80.22 151 3 697076929 NA 436787605 ' 334888Ϊ740 0.83 2609 1 929

39i 76 88.26 136 3 616638209 NA 445686533 ' 3684659067 0.86 2872105746

392 76 81.53 163 3 787771873 NA 436785170 ' 3406043233 0.81 2653439627

393 76 77.94 160 3 743786484 NA 400149982 3267028863 0.81 2538093301

394 76 76.99 167 2 791232195 NA 425292630 3218452032 0.8 2505486700

395 76 70.44 159 2 649080887 NA 373 3 71904 294051793 3 0.82 2292263313

396 76 88.51 156 2 807525774 NA 465511355 3700093284 0.82 2882298970

397 76 82.31 159 2 765889366 NA 445038644 3434735155 0.82 2677109298

398 76 78.32 161 2 749055308 NA 427148026 3267976651 0.81 2546666878

399 76 86.35 143 2 659398886 NA 438117809 3604248950 0.85 2808775371

400 76 97.13 141 2 7Ϊ4439435 ' NA 491919384 4056554429 0.85 3161834109

401 76 94.8 145 2 735037989 NA 481733193 3955807304 0.84 3081892515

402 76 86.71 161 2 836070598 NA 4469221 33 3626989067 0.82 2823534987

403 76 83.27 162 2 794327358 NA 439550249 3480345954 0.81 271 353 5987

404 76 74.73 161 3 700875364 NA 398108732 33 33750876 0.82 2428885174

405 76 83.64 158 2 779529415 NA 444602272 3494896176 0.82 2723700952

406 76 78.46 161 2 763399200 NA 425917643 3278526712 0.81 2553600591

407 76 100.19 131 4 645284716 NA 479119943 4173727392 0.87 3253309528

408 76 74.51 160 2 701049886 NA 387756401 3109536950 0.82 2424864033

409 76 82.32 163 2 801179545 NA 435596113 ' 3434123419 0.81 2678283341

410 76 68.53 162 5 652806087 NA 357151106 ' 2855365200 0.81 2227737545

411 76 77.54 159 2 706124375 NA 404357546 ' 323222773 3 0.82 2521285530

412 76 66.24 158 3 619166078 NA 344927258 2769160535 0.82 2155978071

413 76 69.8 162 4 675525534 NA 383 252895 2914949399 0.83 2270592634

414 76 80.5 159 2 740300262 NA 433459716 3358116395 0.82 2618391438

415 76 68.29 168 2 705919678 NA 367900425 2848350367 0.8 2218669022

416 76 101.41 143 769552403 NA 538007430 4237715175 0.85 3300638500

417 76 79.32 162 2 765552475 NA 403 341975 3318595788 0.83 2580140536

418 76 82.37 162 2 782879519 NA 432812497 3440978690 0.81 2681844314

419 76 73.14 167 2 747459750 ' NA 399637426 3055898457 0.8 2379799753

420 76 77.66 166 5 780033251 NA 421811285 3245369048 0.81 2528594855

421 76 82.61 162 2 803914363 NA 447912333 3450443794 0.81 2689073541

422 76 68.07 165 3 683150468 NA 382187309 2842357740 0.81 221423 1042

423 76 86.4 142 2 660542061 NA 434830787 3607935781 0.85 2807272874

424 76 82.25 163 2 799570239 NA 439388502 3432520179 0.81 2676805555

425 76 84.27 157 2 756556752 NA 424811824 3526659609 0.82 2741487046

426 76 100.17 138 2 723671123 NA 502469367 4184594726 0.85 3260070030

427 76 78.13 166 3 779117736 NA 411315614 3258987234 0.81 2541140206

428 76 77.14 160 3 720368551 NA 409994402 3220065056 0.82 2510996864

429 76 78.99 161 2 762785222 NA 4365Ϊ2483 ' 3297585738 0.81 2570983818

430 76 78.32 163 2 754277739 NA 428776416 ' 3265794408 0.81 2545716934

431 76 59.33 169 3 625965033 NA 328629122 2478522606 0.8 1928812268

432 76 78.48 163 2 755370544 NA 435994177 3272944756 0.83 2551374188

433 76 77.3 163 3 747897797 NA 395774852 3239151626 0.83 2516508030

434 76 75.8 164 5 747017065 NA 400563408 3166358377 0.83 2466127458 Mean Median Min Number

Read Mean insert insert of SNPs On Bait

Length target Size Size Near Bait in Off Bait On Bait vs On Target

AP ('overage INS INS Bases dbSNP Bases Bases Selected Bases

435 76 87.83 158 4 807269663 NA 464597544 3672153277 0.82 2859490165

436 76 81.48 160 2 766914877 NA 4253 38002 3401018824 0.82 2652316142

437 76 79 154 2 679484128 NA 43 3 3 81253 3292473788 0.83 2567781886

438 76 75.23 160 2 714092192 NA 407808213 3143851244 0.83 2448109655

439 76 77.85 161 5 735884398 NA 404356333 3251809283 0.82 2533481505

440 76 75.15 162 2 710737579 NA 3843 16978 3130576373 0.83 2443678774

441 76 69.22 162 3 666398228 NA 360430244 2892044565 0.81 2252040967

442 76 ST.29 160 3 771655591 ' NA 423715348 339Ϊ 126050 0.81 2643204444

443 76 85.06 159 2 768856258 NA 444512000 3542832699 0.82 2767672878

444 76 86.44 153 4 743092965 NA 445037575 3604399111 0.83 2810758347

445 76 71.9 154 3 632359786 NA 379700833 2996351665 0.83 2336351063

446 76 76.51 161 2 736898776 NA 428688467 3392529398 0.81 2486279154

447 76 68.62 165 6 675429885 NA 359689587 2860722850 0.81 2229843942

448 76 80.14 136 2 547652854 NA 404139509 3337894960 0.86 2604839225

449 76 82.23 158 5 752023897 NA 424392375 3430937310 0.82 2673935965

450 76 75.22 158 2 685285264 NA 387285800 3143326475 0.82 2447729499

45 ϊ 76 85.01 154 2 747393239 NA 446171517 3547573849 0.83 2767525530

452 76 71.18 153 2 609822140 NA 374265494 ' 2964964599 0.83 2312871616

453 76 90.93 152 3 778918089 NA 480978760 ' 3797873177 0.83 2959848613

454 76 80.12 160 2 775235343 NA 444023881 ' 3349737742 0.81 2607436058

455 76 78.96 163 2 749136733 NA 43 3430381 3300099439 0.81 2569967070

456 76 77.91 157 2 708900399 NA 4353 37778 3250915180 0.82 2535344799

457 76 80.26 159 4 747710290 NA 430211670 3342538030 0.82 2609754870

458 76 80.92 154 2 708318233 NA 429702452 3373730588 0.83 2630342537

459 76 78.38 157 715661146 NA 444262827 3267485747 0.82 2548231304

460 76 89.45 153 2 783455700 NA 564182899 3736837188 0.83 2912181781

461 76 85.23 155 3 762601313 NA 452710856 3554193015 0.82 2770159815

462 76 189.94 123 1 1087412146 ' NA 863666444 7937924142 0.88 6184566287

463 76 178.74 164 2 1791288903 NA 950377462 7487443456 0.81 5826790865

464 76 174.61 156 1 1635742913 NA 899531985 7338767441 0.82 5689341949

465 76 212.81 145 1 1709401866 NA 1099389766 8883250526 0.84 6929939114

466 76 1 73.82 161 1 1683 380483 NA 957241566 7283684551 0.81 5667985152

467 76 149.97 163 1468174863 NA 806557282 6268316804 0.81 4882982393

468 76 1 83.53 159 1 1723808336 NA 976206125 7682388514 0.82 5977578457

469 76 1 74.28 159 1 1627489440 NA 893094183 73033 82393 0.82 5677745616

470 76 188.04 155 i 1655482019 NA 990222434 7857614787 0.83 6126736760

47 ϊ 76 186.62 156 i 1690692004 NA 977875140 ' 7804038009 0.82 6080076670

472 76 184.35 156 1 1676311734 NA 1032673746 * 7665425977 0.82 6004230340

473 76 174.97 160 1 1665094383 NA 932343372 ' 7315421042 0.81 5699381754

474 76 165.6 159 1 1581631500 NA 885103488 6925165426 0.81 5395021662

475 76 166.7 160 1 1577168033 NA 930692902 6966589853 0.82 5427759233

476 76 185.94 160 1754197956 NA 984968279 7780096325 0.82 6061854243

477 76 140.45 160 i 1369396373 NA 739676323 5881875590 0.83 4571588079

478 76 163.62 157 1 1535577737 NA 883080434 6853165742 0.82 5335875702

479 76 169.49 158 1 1585651003 NA 8863 31179 7092908532 0.82 5521528921

480 76 191.42 158 I 1789068501 NA 1019140136 8006514642 0.82 6237040150

481 76 ^"152.96 160 I 1465160630 ' NA 782018466 64Ϊ8Ϊ58367 0.81 4981031365

482 76 148.17 157 1 1381372896 NA 774082930 6189334888 0.82 4824064698

483 76 188.68 156 1722800260 NA 1009433407 7888703821 0.82 6152354563 84 76 162.11 159 1 1549392776 NA 853144054 6793796327 0.81 5285761295

485 76 1 28.82 155 1 1 370864539 NA 678577990 5379405239 0.82 4193633469

486 76 1 74.02 153 3588704686 NA 925186837 7264370988 0.82 5670303 376

487 76 1 .89 135 1 3534878 NA 8154682 60663306 0.84 47176437

488 76 1 70.25 151 1 1473911403 NA 846478923 7135080239 0.83 5545860156

489 76 182.57 151 i 1578184080 NA 942327715 7629564781 0.83 5946799925

490 76 166.89 148 i 1387232993 NA 841156888 6988949023 0.83 5436098295

49 ϊ 76 157.72 150 i 1372978284 NA 825338856 ' 6601419607 0.83 5Ϊ38457Ϊ95

492 76 189.38 154 1 1692692631 NA 996210581 * 7915938897 0.82 6169292450

493 76 155.74 156 1 1448940697 NA 836496989 6523539846 0.82 5072348777

494 76 179.2 147 1 1490113284 NA 938496806 7493807375 0.83 5836128515

495 76 170.6 146 2 1382576433 NA 889072986 71 19767340 0.84 5558320323

496 76 184.45 148 i 1544934552 NA 839304599 7817303200 0.83 6010360080 Mean Median Min Number

Read Mean Insert insert of SNPs On Bait

Length target Size Size Near Bait in Off Bait On Bait vs On Target

AP ('overage INS INS Bases dbSNP Bases Bases Selected Bases

497 76 183.86 149 1 1558278352 NA 952723435 7686699073 0.83 5990100353

498 76 151.68 350 1 1298653234 NA 776918199 6336873220 0.83 4939984726

499 76 172.72 349 1 1452368346 NA 893 558021 7224807824 0.83 5626887973

500 76 193.29 350 1 1676756603 NA 3009569025 8084459976 0.83 6296590618

50 i 76 176.19 150 1 1502698064 NA 938335921 7363907423 0.83 5738335933

502 76 127.14 1 7 5 10492.33966 NA 648576281 531141.3830 0.84 4138305372

503 76 162.03 154 1 1474917349 NA 829635401 6805670267 0.82 5279107644

504 76 ΪΪ9.58 152 1 1002972764 ' NA 594856324 4988837940 0.83 3891560774

505 76 105.46 162 2 3001635115 NA 534552767 44079Ϊ8074 0.81 3430759723

506 76 98.15 162 2 947585790 NA 508324923 4097922914 0.81 3193359078

507 76 104.69 161 4 990043943 NA 525478792 4383012615 0.82 3408339712

508 76 1 13.33 161 2 3003243691 NA 559956233 4739031416 0.82 3689093142

509 76 96.15 146 2 7453 88002 NA 461384439 4008042714 0.84 3130739597

510 76 1 17.7 145 2 907773858 NA 575725155 4938056947 0.84 3833523 878

511 76 109.04 148 2 8693 76712 NA 524609256 4553017917 0.84 3551464085

512 76 105.67 150 2 873 3 37456 NA 506100999 4437227532 0.84 3441947450

513 76 102.35 158 2 950312034 NA 506302183 4285848500 0.82 3334232208

514 76 106.01 155 2 907900807 NA 5 Ϊ 8778733 ' 4422158315 0.83 3449930517

515 76 108.77 159 2 997751748 NA 536969161 * 4542727625 0.82 3539874983

516 76 104,33 55 3 912003639 NA 499904287 ' 4358687702 0.83 3394526890

517 76 109.63 337 2 725346250 NA 489244861 4556197925 0.86 3567681148

518 76 107.96 347 2 865168044 NA 532976210 4512106228 0.84 3516257577

519 76 122.47 327 2 686728087 NA 520076737 5098020992 0.88 3989462995

520 76 114.48 149 1 954198586 NA 558476860 4789346284 0.83 3730147030

521 76 115.05 154 2 1005768958 NA 563 3 80675 4815904574 0.83 3748929930

522 76 106.87 153 2 935505144 NA 525965359 4471331504 0.83 3481560826

523 76 100.06 167 2 1012429847 NA 494897509 4199105672 0.81 3255216479

524 76 127.08 132 2 79 Ϊ 497687 ' NA 549361569 5306437075 0.87 140103448

525 76 101.62 146 2 824646638 NA 548285233 4377600889 0.84 3292976699

526 76 107.82 150 2 899764499 NA 502996444 4539552191 0.83 3508542221

527 76 104.41 106 2 455348646 NA 530218080 4365666245 0.91 3393033769

528 76 1 30.17 132 2 833418132 NA 588085486 54283 85175 0.87 4239397218

529 76 1 21.57 137 2 832723167 NA 552568332 5073451715 0.86 3958040218

530 76 144.45 126 2 765881863 NA 58098.3650 6004634118 0.89 4707742019

531 76 91.48 157 2 787718291 NA 426296004 38327 J.1502 0.83 2976523760

532 76 132.17 134 2 868571534 NA 584131030 5505199590 0.86 4304190675

533 76 86.16 106 2 353589826 NA 55392Ϊ675 ' 357632346Ϊ 0.91 2 06621506

534 76 118.89 337 2 820889692 NA 559236878 ' 496079Ϊ549 0.86 3871432487

535 76 99.68 346 2 790641849 NA 472277880 ' 4157786225 0.84 3242422348

536 76 102.62 357 2 928185633 NA 486134968 4295440703 0.82 3341723003

537 76 95.95 330 2 625882537 NA 402682853 4002033284 0.86 3125097388

538 76 98.43 362 3 943957258 NA 473738844 4112041 302 0.83 3203100519

539 76 186.3 193 2457846856 NA 1358152440 7751259320 0.76 6067726356

540 76 213.79 182 25304.32307 NA 1248039047 8938735874 0.78 6965203339

541 76 151.32 168 2 1356586693 NA 855366480 6282328253 0.82 4922845662

542 76 98.71 175 2 1105657464 NA 611448812 4126715829 0.79 3211765035

543 76 74.15 133 2 526069638 ' NA 446790877 3100763905 0.85 2411828455

544 76 141.51 149 3 3 384405530 NA 673925808 5909399259 0.83 4608053762

545 76 156.95 147 3 3247947353 NA 753901330 6552060617 0.84 5115367038

546 76 151.63 147 3 3241864981 NA 707291456 6363219812 0.84 4942590587

547 76 341.18 144 3 3 305999942 NA 642747998 5889653169 0.84 4597090892

548 76 3 38.16 147 2 3 329117476 NA 652629708 5773896866 0.84 4503695582

549 76 343.68 147 1 1 369695500 NA 669176754 6007219627 0.84 4683209958

550 76 3 22.51 149 1 1038761037 NA 571067627 5123451228 0.83 3992933934

551 76 110.73 144 2 858119411 NA 517915734 4625379636 0.84 3607176389

552 76 137.82 144 1 1084533697 NA 672101191 5758560736 0.84 4490955130

553 76 120.31 148 2 984928330 NA 557325293 ' 5033259246 0.84 3920673026

554 76 156.96 335 2 1025985372 NA 772795138 ' 6521341067 0.86 5117503962

555 76 108.3 3 343 2 729371320 NA 840462272 4467650002 0.86 3518909402

556 76 153.48 345 2 1185744704 NA 702955185 6332507203 0.84 4936617785

557 76 138.59 347 4 1035723860 NA 703248764 5819820375 0.85 4513110207

558 76 135.45 346 2 1025203736 NA 766845370 5605496603 0.85 4413151695 Mean Median Min Number

Read Mean Insert insert of SNPs On Bait

Length target Size Size Near Bait in Off Bait On Bait vs On Target

AP ('overage INS INS Bases dbSNP Bases Bases Selected Bases

559 76 122.73 152 1 1063113646 NA 575258880 5126823092 0.83 3995735263

560 76 137.81 347 1 1 106153266 NA 646550835 5759075729 0.84 4488435712

56i 76 105.55 347 1 860369480 NA 476260204 4405927384 0.84 3435763559

562 76 135.19 347 i 1099034323 NA 620886763 5667406388 0.84 4402045415

563 76 129.1 1 9 i 1112754243 NA 633280956 5407973743 0.83 4208092945

564 76 128.67 1 7 i 1061738366 NA 627240674 5365515690 0.83 4188675893

565 76 55.58 118 1 329934020 NA 288501094 2320021381 0.88 1806518777

566 76 45.25 102 1 1800Ϊ4776 ' NA 172 11885 1892863064 0.91 1469681425

567 76 201.1 105 1 830587748 NA 889889265 8370962028 0.91 6552266795

568 76 122.43 119 3 693234548 NA 560303055 5329863674 0.88 398483 1820

569 76 196.91 141 3 3497398904 NA 944248995 8234415974 0.85 6418835791

570 76 33.48 1 13 3 202301605 NA 203439634 1432057833 0.87 1087479490

57 S 76 164.61 149 3 3380635131 NA 864697303 68873 15348 0.83 5364966161

572 76 169.49 150 i 1462726604 NA 873428495 7085987751 0.83 5523607178

573 76 16.13 97 i 603 34968 NA 89958975 666060421 0.92 520396923

574 76 1 86.04 139 1 1463144457 NA 836099540 7807589861 0.84 6063289916

575 76 69.57 115 384122996 NA 309269409 2924987827 0.88 2262160127

576 76 139.86 182 1 1723260769 NA 82746577Ϊ ' 5863788434 0.77 4554975857

577 76 142.44 140 1 1144416471 NA 983609977 ' 5954124883 0.84 4637738796

578 76 156.36 150 1 1393620797 NA 840824841 ' 6525979945 0.82 5085284869

579 76 70.17 104 1 295758068 NA 434159942 2917309208 0.91 2282861750

580 76 228.92 3 33 1 1 139032026 NA 2482871430 9551702894 0.89 7458751236

581 76 116.75 363 i 1 161182854 NA 682520622 4875940337 0.83 3795879130

582 76 150.47 157 i 1450648363 NA 872366894 6287850533 0.83 4899917033

583 76 144.1 165 1469812243 NA 832688196 6017448376 0.8 4691245163

584 76 119.83 155 1 1081816060 NA 665076671 4984666982 0.82 3896700600

585 76 163.89 150 1 1455325524 NA 1032982488 6838983529 0.82 5338384044

586 76 148.94 156 1 1415793463 ' NA 877790732 62286Ϊ744Ϊ 0.81 4850702523

587 76 127.2 156 1 1 393373007 NA 765152430 5330604114 0.82 4137991380

588 76 145 155 3 3346945820 NA 804286435 6045283594 0.82 4722958495

589 76 142.79 162 3 3405844650 NA 829655632 5963327298 0.81 4649847398

590 76 1 20.66 154 3 3080594393 NA 677013745 5039797534 0.82 3927399922

59 S 76 1 21.43 131 905883795 NA 643065082 5089746573 0.85 3952554719

592 76 1 32.21 144 i 1 373618963 NA 803460239 5535776224 0.83 4308042167

593 76 160.51 124 1 1054822732 NA 830614295 6749914434 0.86 5223625747

594 76 182.46 146 i 1501132196 NA 1097616342 7613266359 0.84 5947523804

595 76 146.95 102 1 599785543 NA 741143208 ' 61076946Ϊ9 0.91 4786225251

596 76 125.33 94 1 470073147 NA 632966619 ' 5241754762 0.92 4072266308

597 76 129.28 156 1 1248149594 NA 995051952 ' 5400652023 0.81 4209353615

598 76 156.29 329 1 1016779474 NA 754635055 6529826406 0.87 5085200803

599 76 181.09 323 1 1012923024 NA 936468486 7574731642 0.88 5904945264

600 76 176.77 332 i 1155800393 NA 856061833 7396323734 0.86 5761287877

60 i 76 198.28 1 38 i 1000814833 NA 962753638 8252989530 0.89 6467044443

602 76 152.82 122 i 850915634 NA 739287301 6367070069 0.88 4978894341

603 76 183.64 1 33 i 828490164 NA 893375767 7598617754 0.9 5983498852

604 76 161.07 119 1 853503025 NA 822430097 6697565747 0.89 5248517936

605 76 154.06 122 1 849775770 ' NA 695840098 6407278172 0.88 5019942450

606 76 156.89 124 1 879589620 NA 763164204 6529659677 0.88 5110525726

607 76 166.38 135 3 1 336850674 NA 854953896 6922853598 0.86 5425789272

608 76 143 139 3 3009294984 NA 725652753 5944412663 0.85 4658677949

609 76 3 81.71 143 i 430604607 NA 971726372 7579307513 0.84 5925067700

610 76 3 50.41 135 3 3036232366 NA 789691292 6259851709 0.86 4898553 173

611 76 3 85.59 128 i 1 306294003 NA 897081086 7730058274 0.87 6045393940

612 76 365.19 136 1 1 386739845 NA 830022533 6898345770 0.85 5384737490

613 76 183.73 122 i 1042607502 NA 895496498 7670397596 0.88 5991017595

614 76 164.99 118 i 878505067 NA 920281365 6883075377 0.89 5381163368

615 76 180.42 131 1 1138076307 NA 940905567 ' 7493580507 0.87 5 79922019

616 76 150.22 132 1 1028042754 NA 778042546 ' 6256370030 0.86 4889162772

617 76 132.93 323 1 741035345 NA 722478668 5527511103 0.88 4327664861

618 76 125.83 308 1 544656789 NA 723293827 5216452073 0.93 4096967709

619 76 174.42 328 1 1104180430 NA 3004316487 7266110664 0.87 5681813598

620 76 149.55 332 i 101743993 8 NA 773635201 6259797390 0.86 4872976398 Mean Median Min Number

Read Mean Insert insert of SNPs On Bait

Length target Size Size Near Bait in Off Bait On Bait vs On Target

AP ('overage INS INS Bases dbSNP Bases Bases Selected Bases i 76 162.53 162 1626698761 NA 920672366 6792160127 0.81 52937892492 76 144.81 366 149791 3779 NA 839250714 6047678563 0.8 47159209633 76 155.53 360 1504347287 NA 863633219 6501046078 0.83 50689571854 76 148.68 363 1445047439 NA 794574959 6234058696 0.83 48428635835 76 1.33.68 157 1234687826 NA 733369203 558552.3107 0.82 43586340586 76 148.35 163 2 1455505227 NA 833867615 6206071284 0.83 48363556427 76 121.25 162 2 1218034377 NA 671136324 5094087064 0.81 39508524148 76 Ϊ 59.98 159 1 1555364564 ' NA 896691781 6691253058 0.81 52156293889 76 131.34 169 I 1430025818 NA 89695953 3 5505846088 0.79 42795904270 76 149.16 162 I 1489026305 NA 840554197 6239650340 0.81 48628734611 76 169.05 156 I 1549353627 NA 924791887 7070541233 0.82 55133609782 76 167.39 151 i 345332.2638 NA 925767682 6993712.365 0.83 54579370923 76 161.59 154 i 3455761245 NA 958939828 6763 292.790 0.82 52689030534 76 1 29.77 156 1 390353511 NA 8165.39533 5439556694 0.82 42268946915 76 106.89 161 5 1047261405 NA 604367632 4473298140 0.81 34835350086 76 149.46 136 j 1090189476 NA 734656,382 6274493621 0.85 48733947567 76 156.92 156 I 1473287659 NA 822450203 6581877616 0.82 51136581288 76 112.55 187 2 1381106740 NA 695732955 ' 4696554853 0.77 36676831499 76 166.53 126 1069489579 NA 800289647 * 6980235759 0.87 54238120960 76 157.55 128 1029023468 NA 750225338 * 6602377885 0.87 5133152829 i 76 114.39 107 511566092 NA 572259506 4756542285 0.9 37174425412 76 38.28 3 3 3 1 221597569 NA 383970770 1615160230 0.88 3 2.4289177,33 76 161.05 333 i 1063304788 NA 766436847 6712086399 0.86 52506892574 76 166.39 109 i 713786522 NA 800330227 6898302883 0.93 54255946775 76 189.33 1 33 i 880666734 NA 882373211 7872754338 0.9 6I72593S086 76 141.05 119 1 745811812 NA 777329850 5869151861 0.89 45936337657 76 152.17 127 1 923717113 NA 770145933 6330665792 0.87 49527114158 76 257.86 119 1 1486039585 ' NA 1449834977 10794222486 " 0.88 84137296499 76 128.4 116 I 672868019 NA 728404639 5370947689 0.89 41809629350 76 147.4 159 I 1443717276 NA 835697253 6163410396 0.81 4803265915 S 76 3 50.73 157 i 3403 590022 NA 832077487 6,304232.695 0.82 491.34828822 76 3 71.69 114 i 888948944 NA 815132400 7370604719 0.89 55923336283 76 342 155 i 3324157994 NA 805828264 5940773735 0.82 4629323 7864 76 3 59.85 150 5 1357196243 NA 867018066 6668443131 0.83 52064373965 76 82.55 140 3 634308615 NA 570759693 .34253 30762 0.85 268363 51396 76 88.33 144 j 706443095 NA 606928746 3691008690 0.84 28733083497 76 81.77 135 I 559322105 NA 546910423^" ' 3413310539 0.86 26615177318 76 94.64 138 706492767 NA 703785592 ' 3953i)02628 0.85 30791357469 76 90.35 136 623871945 NA 598603025 * 3767(303145 0.86 29388941370 76 73.39 137 529775194 NA 493772603 3062651150 0.85 2386992710 i 76 95.64 333 1 623822764 NA 687304528 39941.37.394 0.86 31137355372 76 81.37 343 i 619546.343 NA 573565454 3399572892 0.85 26490570653 76 74.57 139 2 563510969 NA 53 3 3 57506 3116920795 0.85 2427442.3074 76 78.95 130 i 543445,392 NA 1264856660 3301147237 0.86 25705762035 76 86.35 132 2 5700.34282 NA 560533035 36085.34897 0.86 28118938826 76 81.87 138 2 604277956 NA 540830026 3431485179 0.85 26652088937 76 75.61 137 1 548987134 ' NA 490211647 316553Ϊ905 0.85 24601510098 76 72.92 131 I 473501183 NA 482633063 3043330287 0.87 23705358359 76 127.54 143 I 996875165 NA 879520164 53509Ϊ0234 0.84 41517705440 76 88.83 133 I 595423184 NA 589852709 3735498167 0.86 2892353205 S 76 78.05 137 i 539699532 NA 546589256 .3250949140 0.86 25433079642 76 67.05 138 i 473286612 NA 519668588 2773545035 0.85 23796350423 76 77.56 136 j 555490544 NA 526185823 .3236522015 0.85 25239939554 76 78.81 137 j 564220809 NA 529022933 .3293 594737 0.85 25634789915 76 90.17 137 j 648330954 NA 576503435 3770480103 0.85 29360435476 76 80.15 135 j 551004341 NA 519745440 3353800055 0.86 26091318187 76 62.24 137 } 427137976 NA 374035264 ' 2594 19625 0.86 20220786598 76 83.67 137 565915504 NA 479201807 ' 3495505583 0.86 27235244079 76 77.15 129 480206949 NA 483163741 3227691493 0.87 25104656560 76 79.3 3 343 1 622985335 NA 537660331 33167.38045 0.84 2574577220 i 76 86.69 338 638225878 NA 580712.648 3625029847 0.85 28187444432 76 82.92 333 i 523200252 NA 524285653 3465041768 0.87 2699387817 Mean Median Min Number

Read Mean insert insert of SNPs On Bait

Length target Size Size Near Bait in Off Bait On Bait vs On Target

AP ('overage INS INS Bases dbSNP Bases Bases Selected Bases

683 76 52.47 1 0 400338359 NA 356575943 219097993 3 0.85 1704440893

684 76 65.45 344 1 514571947 NA 409834920 2.739368755 0.84 212.8633917

685 76 134.36 3 59 1 1285737255 NA 739630397 5617820529 0.83 4364434417

686 76 174.89 3 58 i 1664808942 NA 973 209464 7334277664 0.82 5694759155

687 76 170.75 1 59 i 1643249584 NA 1003966662 7169378955 0.83 5566143426

688 76 169.9 1 55 i 1618833485 NA 1 539733463 7138668122 0.82 5538389201

689 76 166.33 154 1 1510610699 NA 8921 12424 6978086790 0.82 542131 1992

690 76 132.09 157 1 1231448956 ' NA 718162589 5541986794 0.82 4302710521

691 76 175.71 154 1 1572683820 NA 95338523 3 7365063775 0.82 5727391 120

692 76 153.98 158 1 1486120589 NA 945570093 6452466545 0.81 5012240960

693 76 146.84 157 1 1400053135 NA 845391843 6167061433 0.81 4785827030

694 76 1 50.23 161 i 3 524398236 NA 832023397 633652.2.152 0.81 489723 5335

695 76 1 56.89 158 i 34962.2.4855 NA 877761434 6590207579 0.81 51 13328681

696 76 1 67.23 159 5 1623231254 N A 909940808 7036542606 0.81 5446463 772

697 76 1 67.67 157 j 1609150054 N A 916946858 7033678190 0.81 5461 593315

698 76 1 23.23 157 1 382175068 N A 679829144 5160010345 0.81 4012043 939

699 76 153.56 156 I 1402779632 NA 821697664 6434973318 0.82 4998955322

700 76 127.26 161 } 125522661 1 NA 728 42688 ' 5340936269 0.81 4141655126^"

70 i 76 102.97 1 7 870439209 NA 803036180 ' 4270405454 0.83 3346795748

702 76 137.95 156 1316121337 NA 1057432634 ^" 5761870578 0.81 4492974265

703 76 137.28 157 1362336793 NA 975482066 5796755533 0.81 447251 1 113

704 76 80.93 305 1 353736560 NA 629990311 3366037358 0.9 2634275074

705 76 122.1 5 349 i 1071610055 NA 933 3 57539 5083531459 0.83 3972888108

706 76 89.56 99 i 334592848 NA 639080011 3706684140 0.92 2914110644

707 76 34.28 85 i 103330743 NA 333 785913 1418641403 0.93 3 11 1 129335

708 76 73.42 97 1 266725688 NA 584985472 30431 10937 0.92 2389373538

709 76 100.94 106 1 439441 157 NA 787787541 4188690058 0.91 3285624650

710 76 68. 14 108 1 3 Ϊ Ϊ236525 ' NA 512315242 2823120931^" 0.9 2215532748

71 1 76 8.6 163 2 89688799 NA 69327733 34900Ϊ469 0.8 270478901

712 76 93.56 1 13 1 483908678 NA 612504472 3934166281 0.89 3043992033

713 76 1 14.73 139 3 836963448 NA 797795455 4756415887 0.85 3737873 553

714 76 1 03.99 152 3 923 493130 NA 7591 14997 4339690954 0.82 3383 546895

715 76 1 2.8.45 159 3 3263 438686 NA 801792362 5397837928 0.81 4180368777

716 76 1 05.8 160 1 1058668504 N A 840277267 4437392728 0.81 3443273 775

717 76 1 17.15 156 1 1 3 3 3833320 N A 863421409 4873491779 0.81 3812304662

718 76 105.27 163 1 1085478268 NA 836745029 4372044510 0.8 3423761819

719 76 104.92 158 1 1035616730 NA 7662Ϊ3646 ' 4379Ό530 Ϊ Ϊ 0.81 3413174934

720 76 1 18 135 1 815510369 NA 783311294 ' 4915(50911 Ϊ 0.86 3843640057

721 76 1 18.33 156 1 1 103164334 NA 49 J G 088 ' 4929107636 0.82 3850768562

722 76 1 19.46 154 1 1070746346 NA 856846343 4963675339 0.82 3887740625

723 76 120.59 3 55 i 1 136142742 NA 878732.565 5059621752 0.82 392.4609204

724 76 144.54 3 54 1343704633 NA 3 305095567 6079205554 0.82 4710934093

725 76 125.87 1 53 i 1236177877 NA 2063632376 5294134365 0.83 4103722653

726 76 1 14.33 142 i 1 128968203 NA 3753 187760 4803122934 0.83 3721689856

727 76 141.59 1 54 i 1343395594 NA 1225726051 5946071993 0.82 4609755892

728 76 106.81 149 1 939372716 NA 900719907 4479500548 0.83 3475930443

729 76 148.0 ί 154 1 1378360639 ' NA 1 132118478 62 Ϊ9436348 0.82 4824164160

730 76 123.37 143 1 1 344751063 NA 2788709384 5183743350 0.82 4019068024

731 76 109.48 143 1 1035158756 NA 2625793536 4603237357 0.82 3568833461

732 76 153.26 145 1 1276497087 NA 1059970303 6433461 196 0.83 4990788426

733 76 3 2.2.82 136 2 3023 835629 NA 2710630347 53 52272372 0.83 40003 87018

734 76 3 48.91 145 2 3287174868 NA 1813473 892 6262638286 0.83 4850997896

735 76 3 48.29 144 1 1226720151 N A 1446066626 6300351372 0.84 4831690679

736 76 3 02.84 150 1 960661517 N A 1247639373 4320633564 0.82 3350332515

737 76 137.01 152 2 1245577035 NA 874085569 5754279106 0.82 4464755360

738 76 1 12.91 136 1 1001614863 NA 3480613502 4747581334 0.83 3682184435

739 76 134.6 142 2 1 195193419 NA 22 Ϊ 8877284 ' 5659802942 0.83 4389463 Ϊ 15

740 76 122.82 130 1 1049370383 NA 4288751723 ^" 5156 10604 0.83 4003313091

741 76 136.33 139 1 1 120749669 NA 1720480042 5731478350 0.84 4443687993

742 76 157.69 344 1259406869 NA 969499701 6612867027 0.84 5134673587

743 76 147.59 349 1287193544 NA 3025602040 6201010708 0.83 481 1768412

744 76 126.52 3 55 i 1 189158440 NA 809949765 5309842825 0.82 4117619247 Mean Median Min Number

Read Mean Insert insert of SNPs On Bait

Length target Size Size Near Bait in Off Bait On Bait vs On Target

AP ('overage INS INS Bases dbSNP Bases Bases Selected Bases

745 76 104,49 139 1 883493009 NA 1463650775 4386983176 0.83 3404101634

746 76 156.33 146 1291718833 NA 1045402550 6562556394 0.84 5091960654

747 76 140.29 139 i 1102156180 NA 3 323181541 5886694386 0.84 4572038683

748 76 133.35 138 i 1136101575 NA 2639821465 5602728436 0.83 4348247966

749 76 114.07 139 i 1043524813 NA 2830361833 4805237988 0.82 3719661172

750 76 130.18 1 2 1104941906 NA 2065145931 5460161675 0.83 4240219470

751 76 120.38 150 2 1050959397 NA 754979512 5056589651 0.83 3919523715

752 76 126.94 148 2 1123781040 ' NA 1186608944 5335636682 0.83 137492564

753 76 109.57 144 1 960014893 NA 1331551288 4593232665 0.83 3566403244

754 76 122.4 141 1 1056983799 NA 1812767484 513996Ϊ 34 0.83 3991505237

755 76 105.9 150 2 908690147 NA 656803230 4438453660 0.83 3445783183

756 76 141.76 152 1 1263228531 NA 983084432 5942933300 0.82 4616743460

757 76 106.59 140 1 928552806 NA 2158450636 4477710262 0.83 3474399588

758 76 140.9 140 1 1 137249524 NA 1532512522 5934485176 0.84 4593622721

759 76 1 4.9 149 1 1 123654267 NA 1268392580 5248958436 0.82 4069798874

760 76 1 31.68 154 2 1219598843 NA 903361929 5533777559 0.82 4290384650

76 ϊ 76 133.45 153 1 1216161941 NA 856675245 5599203527 0.82 4344801052

762 76 143.73 148 1 1243096291 NA 999320625 ' 6024869200^" 0.83 4682327707

763 76 119.59 140 3 1067599734 NA 2777525299 ' 5018513779 0.82 3896637238

764 76 101.55 143 1 895909166 NA 1752569168 ' 42666Ϊ9968 0.83 3309666468

765 76 119.44 145 1 975851062 NA 800475925 5001370098 0.84 3887351249

766 76 104.92 145 858566171 NA 908402093 439996433 3 0.84 3419069907

767 76 137.79 153 i 1245320774 NA 857306835 5788744063 0.82 4490276563

768 76 138.78 154 1293653864 NA 9793 16289 5823111330 0.82 4517708199

769 76 141.03 153 1293342163 NA 1008382650 5917734380 0.82 4591765805

770 76 135.5 151 1210082768 NA 867594313 5691993429 0.82 4416175215

771 76 145.66 148 1250236198 NA 983962700 6123935068 0.83 4749442096

772 76 136.02 154 1251786582 ' NA 853361061 5715507499 0.82 4433305068

773 76 110.54 145 1000749175 NA 1825696666 4642878317 0.82 3602022328

774 76 126.35 146 1 334546314 NA 1853786704 5307542170 0.82 4119569163

775 76 1 25.75 151 2 1099801276 NA 773850369 52733 73117 0.83 4093498353

776 76 1 20.1 152 1 1075907766 NA 721413863 5040041753 0.82 3908535499

777 76 143.62 154 1 1336928861 NA 956132329 6034394782 0.82 4680340721

778 76 99.85 140 1 968617772 NA 3553547497 4196278108 0.81 3256350892

779 76 1 34.63 149 1 1 189250415 NA 1115593582 5655659030 0.83 4389322244

780 76 140.75 153 1 1289620969 NA 940720666 5913300227 0.82 4587524297

781 76 120.5 140 1 1098506017 NA 3089921673 ' 5058717177 0.82 3926580311

782 76 107.35 143 1 1006320839 NA 3328967626 ' 450439Ϊ803 0.82 3497569409

783 76 105.23 144 1 926022462 NA 1599862822 ' 4422762496 0.83 3428498146

784 76 100.48 154 1 930078330 NA 667505637 4217947804 0.82 3270813684

785 76 115.12 153 1054600052 NA 933620609 4828577672 0.82 3747303040

786 76 140.88 152 1266676398 NA 903485174 5928235356 0.82 4592201914

787 76 136.9 153 1249182863 NA 848396127 5750307573 0.82 4461294091

788 76 128.79 152 1162752343 NA 940554179 5409700504 0.82 4195892007

789 76 112.02 148 1058702165 NA 1736625320 46982071 35 0.82 3647966811

790 76 134.61 152 1191582965 NA 797159578 5653030393 0.83 4385089576

791 76 ΪΪ6.65 152 1047577940 ' NA 740006109 4899207524 0.82 3798119515

792 76 141.78 151 1258845386 NA 896984643 5946684671 0.83 4616021257

793 76 113.26 148 982927724 NA 822718884 4756760041^' 0.83 3688787024

794 76 131.1 155 1243356245 NA 956154579 553 3321206 0.82 4271035578

795 76 0.91 150 0 4567918 NA 3911813 20344865 0.82 15638833

796 76 2.44 154 25509966 NA 24293084 93389134 0.78 70270040

797 76 0.81 148 16 3666493 NA 3057482 16658588 0.82 12892330

798 76 1 .22 153 2 8239669 NA 6372609 32695630 0.8 25172361

799 76 1.04 151 5720492 NA 447 193 26150577 0.82 20273177

800 76 1.47 150 36 9071574 NA 7012340 42703527 0.82 33148961

801 76 152.11 176 1843909199 NA 1201881643 ' 639 ί 84469 0.78 4954029943

802 76 146.35 175 1746173602 NA 1077207533 ' 6162779475 0.78 4769662226

803 76 201.36 138 1526585702 NA 1 360121985 8421708838 0.85 6566132505

804 76 114.74 196 1621494539 NA 723536425 4820971483 0.75 3732039719

805 76 5.96 107 43021125 NA 72373802 243958969 0.85 3 86514108

806 76 4.77 107 36352222 NA 49838789 194039059 0.84 347320610 Mean Median Min Number

Read Mean insert insert of SNPs On Bait

Length target Size Size Near Bait in Off Bait On Bait vs On Target

AP ('overage INS INS Bases dbSNP Bases Bases Selected Bases

807 76 129.33 194 1826035507 NA 848279624 5454040887 0.75 4214120236

808 76 39.5 1 37 1 296269373 NA 3052632263 1666602293 0.85 3 283430358

809 76 18.58 327 1 145190336 NA 3 58012621 778193477 0.84 600647644

810 76 140.85 376 i 1701374004 NA 830381832 5906559032 0.78 4583618492

81 1 76 138.25 169 1 1566461674 NA 839341974 5794543565 0.79 4500969624

812 76 144.96 173 2 1708607845 NA 820026569 6099465120 0.78 4716917598

813 76 108. 15 197 1 1584037108 NA 748302783 4541025482 0.74 3513745392

814 76 18.83 134 1 Ι6Ϊ 5Ϊ8059 ' NA 186175729 789046779 0.83 606577437

815 76 154.58 184 1 2041 141882 NA 1255419050 6508396447 0.76 5034482966

816 76 16.47 131 1 166229573 NA 331256308 697974864 0.81 531036820

817 76 4.1 1 1 15 1 28281932 NA 33374506 165084229 0.85 126020843

818 76 1 15.5 142 i 3244135756 NA 568521643 6 4842828216 0.8 3767398544

819 76 i 33.54 1 19 i 9783 91075 NA 5583630474 5559344821 0.85 4354394605

820 76 99.95 143 5 1 300756531 N A 5149058424 41929191 13 0.79 3259623 508

82 ϊ 76 1 8.77 1 18 j 952426598 N A 6046705422 5373 730968 0.85 4198997043

822 76 1 72.31 1 10 j 965756338 N A 4091592309 71 59028614 0.88 5615327159

823 76 1 19.63 131 j 867326350 NA 1847958671 4982033036 0.85 3894924530

824 76 189.1 131 } 1357488842 NA 2082038517 ' 7891600550 0.85 6161 186850

825 76 85.23 1 2 9631 14627 NA 5487598507 ' 3573833884 0.79 2778595032

826 76 1 12.4 137 1 138745530 NA 5997147599 ' 4709325259 0.81 3666158364

827 76 1 16.59 1 4 1 182521832 NA 3739556079 4880590869 0.8 3798924053

828 76 1 15.19 3 3 8 1 903662333 NA 6370253925 4815784033 0.84 3752637826

829 76 1 16.09 342 i 1 184253 596 NA 4703 538249 4861407729 0.8 3783254927

830 76 131.35 145 1 1293491346 NA 3647905174 5501642056 0.83 4284567671

831 76 1 12.59 1 0 1 1044536628 NA 3398991885 4712357923 0.82 3671648280

832 76 184.37 124 1 1096278681 NA 1239978760 7687587936 0.88 6010608118

833 76 124.5 1 15 1 962963623 NA 6902466478 5213360748 0.84 4058923463

834 76 ΙΪ2.28 135 1 1090247235 ' NA 5386106301 4697969090 0.81 3661971081

835 76 125.51 122 1 1038105236 NA 6627672371 524348Π67 0.83 4093636793

836 76 134.67 120 1 946593622 NA 4498920443 563 3081599 0.86 4391840560

837 76 1 42.76 153 i 3383497670 NA 17726443 87 5978429093 0.81 46553 83 628

838 76 1 74.62 125 i 3242185736 NA 3343547372 7289331423 0.85 5690742210

839 76 1 35.86 150 i 3243 469121 NA 1351975466 5683 577309 0.82 4430264580

840 76 96.26 124 j 823 878980 N A 4859794029 4025222164 0.83 3138229754

84 ϊ 76 1 47.37 126 1 33251 1834 N A 4487528389 6146549571 0.84 4801033853

842 76 104.95 139 I 1052674356 NA 4192361798 4400931641 0.81 3419069834

843 76 100.57 139 } 1045712474 NA 5089369218 ' 4213793635 0.8 3277268046

844 76 68.69 1 0 685428560 NA 2722774500 ' 28690 Ϊ4757 0.81 2234899703

845 76 1 13.98 138 1 1062651 343 NA 3878069188 ' 4761513862 0.82 3713108017

846 76 122.26 154 2 1 134687369 NA 863269905 5101489788 0.82 3975498680

847 76 87.56 339 1 887914655 NA 4303330959 3666716348 0.83 2851005770

848 76 100.64 3 37 i 752527435 NA 4309428440 4200035745 0.85 3280824353

849 76 107.06 132 i 1034519390 NA 4904599956 4499201232 0.83 3488239074

850 76 103.49 1 0 1 886630773 NA 1660397792 431982083 5 0.83 3369732579

851 76 134.53 143 1 1262963520 NA 3386838676 5625781340 0.82 4383677565

852 76 1 15.84 123 1 863505040 NA 3789383867 4834134288 0.85 3772007814

853 76 164.38 109 1 956906453 ' NA 3834183339 6908869911 0.88 5353434846

854 76 1 14.62 1 13 1 833870779 NA 4743295637 4769732796 0.85 3733423292

855 76 72.58 122 1 678266713 NA 2652628289 3063 Π7074 0.82 2362959932

856 76 83.07 121 1 753007419 NA 3135336743 3498398671 0.82 2705372502

857 76 57.2 1 13 i 536046763 NA 3443506993 2436706188 0.82 1862263 890

858 76 73.61 121 i 640647179 NA 3504952048 30865933 19 0.83 2397466183

859 76 1 00.03 121 2 832391024 N A 2918548668 41953 58366 0.84 3260753186

860 76 1 90.59 132 1 1273 955210 N A 1 106386284 7942075262 0.86 6210734531

86 ϊ 76 1.09 140 2 6352166 NA 13528002 28646551 0.82 22258951

862 76 99.21 121 i 921377619 NA 5502074916 41721 11823 0.82 3235580809

863 76 173.07 159 i 1660416963 NA 974918891 * 72693 Ϊ8592 0.81 5632535119

864 76 160.34 152 1 1432742667 NA 930181489 ' 6728260338 0.82 5213928626

865 76 178.43 1 9 1 1526723676 NA 960536249 7514996847 0.83 5815560432

866 76 174.03 3 56 1649740228 NA 994759329 7324750795 0.82 5674000285

867 76 127.52 344 i 102713633 8 NA 6843 13540 5347333676 0.84 4147953375 Oxidation PF HQ PF HQ PF HQ PF HQ PF HQ PF HQ

Error Rate Oxidation Aligned Aligned Aligned Q20 Aligned Q20 Aligned Aligned

Organism OXO Q OXO Bases AP Bases Bases AP 3¾ases Reads AP Reads

Human 2.00E-04 37.10871 10897725192 10897725192 10794436123 10794436123 145182605 345182605

Human 0.0001 1 39.42023 9883680140 9883680140 9775796578 9775796578 131852039 333 852019

Human 2.00E-05 47,60946 9937705420 9937705420 9839543973 9839543973 133928766 133928766

Human * 9.66E-05 40,63834 9686430636 * 96T6430636 9596375973 9596375973 128998640 128998640

Human 0.00012 39.29792 9760699586 ' 9760699586 9666888845 9666888845 129960424 129960424

Human l.OOE-05 48.47005 8620847907 ' 8620847907 8535290232 8535290232 1 34822373 114822373

Human 7.00E-05 41.5906 9183521832 9183521832 9092655598 9092655598 122317499 122317499

Human 3.00E-05 45.02501 7717221487 7717221487 7639440104 7639440304 302839161 102839363

Human 4.00E-05 44.39537 9010908467 9010908467 8923262392 8923262392 320067639 120067639

Human 0 79.1959 8161 139630 8161139630 8067654433 8067654433 108945603 108945603

Human 7.00E-05 41.87843 9843649924 9843649924 9747011854 9747011854 132997267 132997267

Human 2.00E-05 47.14795 9516374676 9516374676 9426771639 9426771639 126698506 126698506

Human 2.00E-05 46.57158 7516611706 7516611706 7439581747 7439581747 100214116 100214116

Human 3.00E-05 44.7Ϊ443 ' 9790953690 9790953690 ' 9699686236 9699686236 130300372 130300372

Human 0.00013 38.72638 * 8842780459 8842780459 ' 8761097828 8761097828 117783305 3 17783305

Human 4.00E-05 43.52726 10078599694 10078599694 9970291403 9970291403 134975046 334975046

Human 4.00E-05 44.46856 9677756459 9677756459 9576248999 9576248999 130127463 330127461

Human 4.00E-05 43.6327 9229729132 9229729132 9139105123 9339105123 124043578 3 24043578

Human 1.00E-05 52.37736 9772740364 9772740364 9682211549 9682211549 130001900 330001900

Human 0.00016 38, 10581 8286221699 8286221699 8202042045 8202042045 110421756 3 30421756

Human 0.00021 36,75304 9709186443 9709186443 9613063518 9633063518 129399223 329399223

Humaii 4.00E-05 43,72046 9510619526 9510619526 9428199248 9428199248 126497202 126497202

Humaii 6.00E-05 42,21887 8234158202 8234158202 8159065753 8159065753 109543036 109543036

Human ' 0 54,00676 8116452033 ' 8116452033 8027849641^" 8027849641 108278036 108278036

Human 3.00E-05 45.17063 8758614714 ' 8758614714 8679592874 8679592874 1 36525169 116525369

Human 5.00E-05 43.0983 8395840041 8395840041 8333488245 8313488245 1 3 3895948 111895948

Human 1.00E-04 39.88768 8782289199 8782289199 8693934655 8693934655 3 37040728 117040728

Human 0 79.29863 8238984820 8238984820 81563 21394 8156123394 309772249 109772249

Human 4.00F.-05 44.35743 1 1013719372 11013719372 10934293153 109142933 53 347488570 147488570

Human 3.00E-05 45.34517 10890559226 10890559226 10795482870 10795482870 145990240 145990240

Human 5.00E-05 43.23147 8605525269 8605525269 8523777046 8523777046 1 35391227 115391227

Human 0 79.66926 9252462836 9252462836 9161465584 9161465584 123247249 123247249

Human 3.00E-05 45.37316 ' Ϊ0050605543 10050605543 *^" 9955978694 9955978694 134404804 134404804

Human 0.00013 38.88096 * 10263143371 10263143371 ' Γθ 166422227 10366422227 137133003 337133001

Human 4.00E-05 43.92059 ' 9941272042 9943272042 ' 9846553007 9846553007 134453679 334453679

Human 3.00E-05 45.89368 11008492052 11008492052 10907886826 10907886826 147788436 347788416

Human 0.00016 38.09279 9145017375 914501 7375 9042132085 9042132085 122073795 3 22073795

Human 4.00E-05 44.6155 9988687357 9988687357 9892650438 9892650438 134133887 334133887

Human 0 59,55698 11792301449 11792301449 11657888753 1 3657888753 157802233 3 57802233

Human 5.00E-05 43,26029 9979966698 9979966698 9889399330 9889399310 133658532 333658512

Human 4.00E-05 43,89635 9429541003 9429541003 9339015453 9339015451 126435947 326435947

Human 4.00E-05 44, 1736 9579479814 9579479814 9489978019 9489978019 128184315 128184315

Human ' 4.00E-05 43,64493 10570000841^" ' Ϊ057000084Ϊ 10473530501^" ' 10473530501 14209Ϊ682 142091682

Human l.OOE-04 39.82256 9074315594 ' 9074315594 897348Ϊ436 8973481436 123 127166 121127366

Human 7.00E-05 41.79395 8280633005 ' 8280633005 81903 87030 8190187030 1 30487539 110487539

Human 6.00E-05 42.38879 8456322428 8456322428 8372419247 8372419247 1 32651974 112651974

Human 0.00015 38.29226 8682556949 8682556949 8598306411 859830643 3 3 35692971 115692973

Human 0.00015 38.18997 8661 542647 8661542647 8566493461 8566493463 3 35570057 115570057

Human 0.00014 38.71007 7808839997 7808839997 7732308712 7732108732 103955031 103955033

Human 0.00012 39.18486 8414722158 8414722158 8330478706 8330478706 1 32364406 112164406

Human 0.00014 38.57589 8516158274 8516158274 8426376494 8426376494 113531858 113531858

Human 0.00015 38.16538 8513859080 8513859080 8426772475 8426772475 113430431 113430431

Human 0.00014 38.57235 ' 8595355125 8595355125 * 8503197227 8503197227 114594845 114594845

Human l.OOE-04 39.9665 ' 9737412322 9737412322 ' 9623779300 9623779300 132202574 332202574

Human 4.00E-05 44.33311 10146437515 10146437515 10048073320 30048073120 135332434 335332414

Human 0 79.19756 9591890059 9591 890059 9500221249 9500221249 128341543 3 28341543

Human 4.00E-05 44.61028 9956333405 9956333405 9869125236 9869125236 132711428 332711428

Human 0 78.49706 8228670297 8228670297 8148905369 8348905169 109544633 309544613

Human 0.00014 38,44932 6952025896 6952025896 6812809384 6832809384 96598745 96598745

Human 2.00E-05 46,87958 8859964751 8859964751 8772347005 8772347005 118512852 3 38512852

Human 0.00012 39, 14416 5024083074 5024083074 4707514082 4707514082 71246794 71246794

Human ' 0 78,47908 720 Ϊ 720664 ' 7201720664 7162803166 7162803166 9543326 95433261

Human 0 78.62749 7736704380 ' 7736704380 7696096283 7696096283 102494478 102494478 Oxidation PF HQ PF HQ PF HQ PF HQ PF HQ PF HQ

Error Rate Oxidation Aligned Aligned Aligned Q20 Aligned Q20 Aligned Aligned

Organism OXO Q OXO Bases AP Bases Bases AP Bases Reads AP Reads4 Human 0 78.88573 6474727583 6474727581 6436935266 6436935266 85894455 858944555 Human 3.00E-05 45.91835 7298780102 7298780102 7251505162 7253 505162 97691963 976919616 Human 3.00E-05 45,21777 7267659774 7267659774 7209359869 7209359869 98152083 981520837 Human * Ϊ.00Ε-05 49,96891 7603673252 ' 7603673252 7562128868 7562128868 100873647 1008736478 Human l.OOE-05 51.4286 7712722621^" * 7712722623 767058Ϊ393 7670583393 302293763 1022937639 Human l.OOE-05 53.28647 6709254282 ' 6709254282 6672245184 6672245384 88997039 889970390 Human l.OOE-05 51.181 33 6982133026 6982133026 6944441209 6944443209 92618695 92618695! Human 0 79.71018 9387367645 9387367645 9336722154 9336722354 3253 12.1 11 1251 323 3 32 Human 0 77.31224 5888327692 5888327692 58553 84402 5855184402 78098403 780984033 Human 9.00E-05 40.52326 9622527412 9622527412 9566343778 9566143778 127718051 1277180534 Human 7.00E-05 41.60681 4473937624 4473937624 4455606494 4455606494 59393627 591936275 Human 6.00E-05 42.62597 9493278403 9491278403 9434463976 9434463976 125960266 1259602666 Human 5.00E-05 43.10462 9443181151 9443181151 9326195205 9326195205 127427559 1274275597 Human 4.00E-05 44.237 Ϊ5 ' 9791192195 9791192195 ' 9656701911 9656701911 132260135 1322601358 Human 3.00E-05 45.96635 ' 9711041325 973 304Ϊ325 ^ 959Ϊ52Ό854 9591520854 130863938 3308639389 Human 3.00E-05 45.09601 9122817583 9322817581 9010855284 9030855284 123079809 3230798090 Human 6.00E-05 42.2.8445 8344768723 8344768721 8239495022 8239495022 1 12468602 3 324686021 Human 0 79.9365 9886311032 988633 1012 9766480269 9766480269 133169623 3331696232 Human 4.00E-05 44.2.8811 9627867433 9627867433 9512005347 953 2005347 129789088 3 297890883 Human 3.00E-05 45.49382 8929514179 8929534179 8820825976 8820825976 120316548 3203165484 Human 6.00E-05 42.37642 8903680980 8903680980 8794577978 8794577978 120001443 3200014435 Humaii 2.00E-05 46,40748 9015583396 9015583396 8907902496 8907902496 121492077 1214920776 Humaii l.OOE-05 49, 17366 9376451952 9376451952 9263630317 9263630317 126207328 1262073287 Human ' 0 63,81223 8508075058 ' 8508075058 8391325616 8391325616 11478 187 1147881878 Human 8.00E-05 41.24202 9084306032 ' 9084306032 89680Ϊ4163^" 8968014363 322681760 1226837609 Human 2.00E-05 47.01368 9409898701 9409898703 9295543707 9295543707 326815067 1268350670 Human 2.00E-05 47.63734 8707284143 8707284343 8585356014 8585356034 3 37675847 117675847! Human 2.00E-05 46.91901 7744954389 7744954389 7640981016 7640983036 30452.0951 1045209532 Human 2.00E-05 46.47513 7729007447 7729007447 7632210796 7632210796 304051287 1040532873 Human 0 79.51667 8762064000 8762064000 8654395126 8654395326 1 383 77128 1181773284 Human 6.00E-05 42.53181 9539486920 9539486920 9426497782 9426497782 128613021 1286130235 Human l.OOE-05 50.77023 8341020581 8341020581 8221547199 8221547199 112720318 1127203186 Human l.OOE-05 50.84452 ' 8614176348 8614176348 ' 85044084Ϊ5 8504408415 116020008 1160200087 Human 3.00E-05 45.46153 ' 8213803674 8233803674 * 8112914766 83 32914766 110643325 3 106433258 Human 8.00E-05 40.75695 ' 8614428139 8634428119 ' 8508Ϊ39695 8508139695 116257359 3 162571599 Human 8.00E-05 40.80274 9469854369 9469854369 9350494234 9350494234 127859520 32785952000 Human 7.00E-05 41.30408 9794885760 9794885760 9683058498 9683058498 131958643 33395864101 Human 3.00E-05 45.39203 9042688576 9042688576 8937872422 8937872422 121754039 3 23 75403902 Human 0 53.88395 1107259493 5 11072594915 1092989723 3 10929897211 149354944 34935494403 Human 0 53.49122 7720257594 7720257594 7617826569 7637826569 104142188 30414218804 Human 6.00E-05 42.3694 9327885353 9327885353 9221649380 9223649380 125631103 32563110105 Human 0 79,29802 8675792896 8675792896 8566328423 8566328423 116894890 11689489006 Human ' o.ooo ii 39,42129 8934815135 ' 8934815135 8826923285 8826923285 1203Ϊ6764 12031676407 Human 4.00E-05 43.6683 89525Ϊ 0520 ' 8952510520 8843 3 45378 8841145378 320692695 12069269508 Human 9.00E-05 40.29684 Ϊ8356923829 ' Ϊ8356923829 Ϊ8343584503 ' 18143584503 247080565 24708056509 Human 2.00E-05 46.7136 8727834535 8727834535 8624157700 8624157700 3 37605781 11760578110 Human 7.00E-05 41.64909 8005042.278 8005042278 7903803341 7903803343 308032.462 1080324621 1 Human 3.00E-05 45.11747 9303 853263 9101853263 898972.0058 8989720058 322749519 12274953912 Human l.OOE-05 48.7789 7837473545 7837473545 7740927348 7740927348 105684628 10568462813 Human 5.00E-05 43.21372 7363 589102 7361589102 7269782977 7269782977 99075075 9907507514 Human 0.00011 39.44045 8850439608 8850439608 8737095410 8737095410 119343682 11934368215 Human 2.00E-05 46.58828 9389407927 9389407927 9273341420 9273341420 126558732 12655873216 Human 6.00E-05 42.3633 ' 9377127194 9377127194 ' 9268597969 9268597969 126315850 12631585017 Human 6.00E-05 42.61847 ' 8002Π0846 8002110846 ^ 7906466745 7906466745 107870335 30787031518 Human 3.00E-05 45.26794 9901267290 9903267290 9765865397 9765865197 133780627 33378062719 Human 6.00E-05 42.63448 9101247738 9303 247718 8988696202 8988696202 122675663 3 2267566320 Human 6.00E-05 42.59455 8976965943 8976965941 8865963062 8865963062 121055323 3 2305512321 Human 3.00E-05 45.37053 9878297638 9878297638 9737012605 9737012605 133609999 33360999922 Human 0 54.49695 8130542644 8130542644 8034212796 8034212796 109412838 30941281823 Human 0 53.86819 8531669280 8533669280 842856083 3 8428560811 114957452 3 3495745224 Human 2.00E-05 46, 17037 8163059187 8163059187 8061610810 8061610810 110040521 11004052125 Human * Ϊ.00Ε-05 48,70923 9730708667 ' 9730708667 96Ϊ4Ϊ88379 9614188379 131168632 13116863226 Human 4.00E-05 43.65703 8445268472 ' 8445268472 8332776402 8332776402 3 33849313 113849313 Oxidation PF HQ PF HQ PF HQ PF HQ PF HQ PF HQ

Error Rate Oxidation Aligned Aligned Aligned Q20 Aligned Q20 Aligned Aligned

Organism OXO Q OXO Bases AP Bases Bases AP 3¾ases Reads AP Reads

Human 0.0001 1 39.76611 8600787976 8600787976 8487016187 8487016187 1160701 33 3 36070113

Human 1.00E-05 48.40952 9135724627 9135724627 9018004437 9038004417 123424936 323424916

Flu man 0 78,9748 8423568692 8423568692 8311082998 8311082998 113547347 113547347

Flu man ' 0 79,03151 825 Ϊ53Ϊ500 ' 8251531500 8153ΪΪ6929 8153116929 1 Ϊ 1046301 111046301

Human 0.00015 38.35626 715756802 ^" 715756802 0 0 10329959 10329959

Human 6.00E-05 41.9488 8700799558 ' 8700799558 8589320266 8589320266 1 37601019 117601019

Human 2.00E-05 48.36203 5183521953 5181521953 5109268209 5109268209 70335411 7013543 1

Human 2.00E-05 47.18164 6886571421 6886571423 6796214896 6796214896 92968524 92968524

Human 0 56.22644 55S 5029995 5515029995 5442318405 5442318405 74346369 74346369

Human 0 75.10471 591 3398795 5911398795 5830712238 5830712238 79852079 79852079

Human 0.00027 35.65627 10192392371 10192192373 10073959384 10073959384 137255889 137255889

Human 2.00E-05 48.38397 11564400055 11564400055 11403704639 11403704639 156079371 156079373

Human 1.00E-05 50.99353 8349448823 8349448823 8246828549 8246828549 112383326 112383326

Human 2.00E-05 46.83221 ' 8409021599 840902Ϊ599 ' 82997569Ϊ4 8299756914 113423429 113423429

Human 3.00E-05 45.887 ' 9002786! ί 9 9002786119 * 8892646982 8892646982 121277178 323277178

Human 0 74.1418 9640083860 9640083860 9513469330 9533469310 130196622 330196622

Human 0 76.17854 1065828393 5 10658283915 10440770639 30440770619 145343558 345343558

Human t .OOE-05 48.42103 10813570636 10833570636 1065495033 5 30654950315 146325809 346325809

Human 2.00E-05 46.40641 8580874056 8580874056 8464212763 8464212763 1 15911470 3 35911470

Human 2.00E-05 46,40937 9237185613 9237385613 9125814745 9325814745 124520997 324520997

Human 2.00E-05 46,51245 9725330263 9725330261 9606701764 9606701764 131055659 333055659

Humaii 0 73,95652 8115459957 8115459957 8013736801 8013736801 109546991 109546991

Humaii 0 74,39102 3100524389 3100524389 3040545979 3040545979 42293033 42293033

Human * 2.00E-04 36,91581 9844583286 ' 9844583286 9757539145 9757539145 13 Ϊ ^"106223 131106223

Human 0.00021 36.77095 6598582741 ' 6598582743 6544257976 6544257976 87790419 87790439

Human 0.00019 37.12285 11756273640 11756273640 11654069097 11654069097 156492268 156492268

Human 0.00019 37.3325 9609061810 9609061830 9529213581 9529213583 327880533 127880533

Human 0.00018 37.34086 10094600804 30094600804 10007647598 10007647598 334368614 134368634

Human 0.00022 36.63456 10349664040 10349664040 10263393927 10263393927 337692329 137692329

Human 0.00025 36.0102 24323985900 24323985900 23983 559455 23981559455 325305121 325305323

Human 0.00022 36.6261 1 10264447387 10264447387 10375499330 10175499330 136609085 136609085

Human 0.00019 37.33679 10955711964 10955711964 10865403091 10865403091 145714617 145714617

Human 0.00022 36.6729 ' 7065304286 7065304286 ' 7010144234 7010144234 93940415 93940415

Human 2.00E-04 37.10974 ' 9820403965 9820403965 * 9737299849 9737299849 130696320 330696320

Human 2.00E-04 37.10501 * Ϊ0728445066 10728445066 ' 10637168293 10637168291 142799092 342799092

Human 0.00019 37.2364 10404367765 10404367765 10318930484 10318930484 138429566 338429566

Human 0.00019 37.26877 10298272443 10298272441 10213210349 3023 3210349 137007385 337007385

Human 0.00022 36.68451 10551427764 10551427764 10464162373 30464162371 140396236 340396236

Human 0.00019 37,34 9887815396 988783 5396 9796596953 9796596953 131760693 333 760693

Human 2.00E-04 37,03344 11086056300 11086056300 10989957763 10989957761 147631597 347631597

Human 0.00019 37, 15899 10549423740 10549423740 10463567062 10463567062 140366179 340366179

Human 0.00019 37,31116 8315632733 8315632733 8242225728 8242225728 110739020 110739020

Human ' 0.00026 35,93118 11768787269 ^" ΪΪ768787269 Ϊ 1672496184 ' 11672496184 156547645 156547645

Human 0.00022 36.68362 1053 344373!) * Ϊ051 Ϊ443730 10426896029 ' 10426896029 139808588 139808588

Human 0.00018 37.37223 5807Ϊ 3 Ϊ8ί ί ' 580711181 3 5759525703 5759525703 77274178 77274178

Human 0.00019 37.21236 10934968830 10934968830 10840141837 10840143837 145575185 145575385

Human 0.00018 37.43753 7739161449 7739161449 7673 508017 7671508037 303086526 103086526

Human 0.00022 36.51832 9232694300 9232694300 9353433648 9151433648 322993524 122993524

Human 2.00E-04 37.02466 10368223208 10368223208 10283212932 10283212932 137982059 137982059

Human 0.00021 36.70199 11593244634 11593244634 11500600435 11500600435 1543 80659 154180659

Human 2.00E-04 36.90172 10224437145 10224437145 10121987616 10121987616 136470840 136470840

Human 0.00019 37.29995 9029302760 9029302760 8947002597 8947002597 120304902 120304902

Human 0.00021 36.73233 ' 9553280360 9553280360 ' 94706 Ϊ 7202 9470617202 127181462 127181462

Human 2.00E-04 37.06759 ' Ϊ069 083499 Ϊ 0699083499 ' Ϊ0607077394 10607077394 142444493 342444493

Human 0.00021 36.79195 11282743322 11282743322 11193528953 1 3 393528953 150071233 350071233

Human 0.00019 37.13694 9517806076 9537806076 9441979428 9443979428 126621667 3 26621667

Human 2.00E-04 37.01379 19075418689 19075418689 18766320284 38766320284 255794530 255794510

Human 0.00018 37.48129 9744728962 9744728962 9655963537 9655963517 129793306 3 29793306

Human 0.0001 8 37,34863 10106718196 10106718196 10026275936 10026275916 134405722 334405722

Human 0.00019 37, 1643 9962246508 9962246508 9877944472 9877944472 132595205 332595205

Human 0.00022 36,66312 11190412436 11190412436 11097191532 11097191532 148928712 148928712

Human ' 0.66021 36,82875 9182539301^" ' 9182539301 9102 I 46015 9102146015 122298875 122298875

Human 0.00021 36.69177 8857408452 ' 8857408452 87833Ϊ4883^" 8781314883 1 37919570 117919570 Oxidation PF HQ PF HQ PF HQ PF HQ PF HQ PF HQ

Error Rate Oxidation Aligned Aligned Aligned Q20 Aligned Q20 Aligned Aligned

Organism OXO Q OXO Bases AP Bases Bases AP 3¾ases Reads AP Reads

390 Human 0.00022 36.55446 23147245032 23147245032 22833694964 22833694964 309357332 309357312

391 Human 2.00E-04 37.11064 10595070666 10595070666 10511857725 1053 1857725 140852988 340852988

192 Human 0.00019 37, 14277 8572981377 8572981377 8499679404 8499679404 114128008 114128008

193 Human * 2.00E-04 36,9481 10661434919 ' ^"10661434919 10572782044 ' 10572782044 141852626 141852626

194 Human 2.00E-04 36.93873 103841 24262 ' Ϊ038 124262 10296174305 ' 10296174305 138232652 138232652

195 Human 0.00023 36.33796 10232579422 ' Ϊ0212579422 Ϊ03263Ϊ1897 ' 1012631 3897 135961187 135961 387

196 Human 0.00021 36.80608 9117414680 9117414680 9037763384 9037763384 123405015 121405015

197 Human 0.00024 36.2789 21532479525 21532479525 23200612117 212006323 3 7 288463291 288463293

198 Human 9.00E-05 40.54093 981 1936182 981 1936182 9728684680 9728684680 130585088 130585088

199 Human 2.00E-04 37.04997 10031950473 10031950473 9953095976 9953095976 133322542 133322542

200 Human 0.00022 36.58973 11274427466 11274427466 11 384579767 11184579767 149883928 149883928

201 Human 0.00019 37.15164 10713435558 10713435558 10636677670 10616677670 142670310 142670330

202 Human 0.00021 36.81233 10919039340 10919039340 10829754434 10829754434 145204222 145204222

203 Human 0.00021 36.77845 * 10436002791 Ϊ043600279Ϊ ' Ϊ0347051206 10347051206 138864028 138864028

204 Human 0.00014 38.42491 ' ϊί08ΐΎό4484 Ϊ 1081764484 ' Ϊ0971511894 10971511894 147813170 347813170

205 Human 1.00E-04 40.08772 9103779736 9103779736 9028361059 9028361059 121176634 321176614

206 Human 2.00E-04 36.9621 9045600660 9045600660 8970476478 8970476478 120301946 3 20301946

207 Human 0.00018 37.44096 10423682305 10423682305 10336093370 30336091370 138663069 338663069

208 Human 0.00019 37.16066 1070083371 2 10700833712 10604740853 30604740853 142516386 342516386

209 Human 2.00E-04 37,09665 9894271878 9894271878 9805368770 9805368770 131722560 333 722560

210 Human 0.00014 38,44225 6935074632 6935074632 6874949164 6874949164 92300812 92300812

211 Humaii 2.00E-04 36,92009 12863323938 12863323938 12682529481 12682529481 171956096 171956096

212 Humaii 0.00023 36,47221 9853774505 9853774505 9767292094 9767292094 131187355 131187355

213 Human ' 0.66022 36,66029 9345675723 ' 9345675723 92696Ϊ8986 9269618986 1242545 Ϊ7 124254517

214 Human 0.00021 36.79624 1025600780!) ' Ϊ0256007800 10373 857936 ' 10171857936 136388707 136388707

215 Human 0.00022 36.57262 10026337535 10026337535 9939466451 9939466451 133454071 133454071

216 Human 2.00E-04 36.99042 10568266835 10568266835 10480678037 10480678037 340582071 140582073

217 Human 0.00019 37.24212 10656475293 10656475293 10566307894 10566307894 343790893 141790893

218 Human 2.00E-04 36.93964 10591883385 10591883385 10497701063 10497703063 343053660 141053660

219 Human 0.00018 37.56148 10423556747 10423556747 10336640398 10336640398 138654826 138654826

220 Human 0.00019 37.18898 5647341823 5647341823 5603224576 5601224576 753 3 8906 75118906

221 Human 0.00023 36.46147 4376856307 4376856307 4339021642 4339021642 58289054 58289054

222 Human 0.00018 37.57414 ' Ϊ0472681739 10472681739 ' Ϊ0389096946 10389096946 139202778 139202778

223 Human 0.00019 37.13883 ' 8972600185 8972600185 ' 8896715264 8896715264 119407705 3 19407705

224 Human 0.00021 36.83168 ' 9111208462 911 3208462 ' 9029526876 9029526876 121346996 321346996

225 Human 0.00024 36.28211 9427203884 9427203884 9347256003 9347256003 125499633 325499631

226 Human 0.00023 36.34439 23241969885 23243969885 22887008800 22887008800 311267483 33 3 267483

227 Human 0.00023 36.36397 11289666955 1 1289666955 11 195783033 3 3 395783013 150151596 3 50151596

228 Human 2.00E-04 36,97972 9121968860 9123968860 9037529843 9037529843 121513399 323 513399

229 Human 0.00022 36,60022 9961530519 9963 530519 9880399882 9880399882 132456258 332456258

230 Human 0.00021 36,78601 11443933235 11443933235 11350313287 1 3350313287 152190838 3 52190818

231 Human 0.00022 36,55954 9980889184 9980889184 9898729371 9898729371 132773215 132773215

232 Human ' 6.66027 35,74502 8882980344 * 8882980344 8804727082 8804727082 118266054 118266054

233 Human 0.00026 35.92527 21758941129 ' 21758941129 21423 Ϊ43240 " 21423143240 293380531 291380531

234 Human 0.00023 36.43734 Ϊ 1436473669 ' Ϊ1436 73669 Ϊ 1347552827 ' 11347552827 152003506 152003506

235 Human 5.00E-05 42.65288 10967858794 10967858794 10779887950 10779887950 147479421 147479421

236 Human 7.00F.-05 41.83095 9693050277 9693050277 95323 83624 9532183624 329938107 129938307

237 Human 0 75.76557 3163439612 3163439632 3302944016 3102944036 43969674 41969674

238 Human 0 75.80982 3288965417 3288965417 3225330976 3225330976 4363 7716 43617736

239 Human 0 76.083 3376456238 3376456238 333 3251542 3311251542 44804444 44804444

240 Human 0.00011 39.64935 10307369431 10307369431 10137877708 10137877708 138190576 138190576

241 Human 0 76.05418 3405959989 3405959989 3341480370 3341480370 45199971 45199971

242 Human 4.00E-05 43.78794 * 6963334663 6963334663 ' 688398786Ϊ 6883987861 92271051 922710 1

243 Human 0.00024 36.1344 * 10336048951 10336048951 ' Ϊ0Ϊ6Ϊ8Ϊ2252 10361812252 138883800 338883800

244 Human 0 75.89472 3227499694 3227499694 3165572097 3365572097 42824740 42824740

245 Human 0 76.32114 3489317764 348933 7764 3423165457 3423165457 46291747 46291747

246 Human 0 76.11214 3382688957 3382688957 3317658363 3337658363 44875332 44875332

247 Human 0 76.20898 3355985756 3355985756 3292044300 3292044100 44532724 44532724

248 Human 5.00E-05 43, 12665 8074424532 8074424532 7936614586 7936614586 107787485 307787485

249 Human 0 75,84945 3225150728 32253 50728 3163906443 3363906441 42779348 42779348

250 Human 4.00E-05 44, 18166 8049103376 8049103376 7912239510 7912239510 107663426 107663426

251 Human ' 0.00021 36,77052 9733426407 * 9733426407 9567Ϊ67668 9567167668 131222096 131222096

252 Human 0 60.46528 8749542952 * 8749542952 8656637013 8656637033 1 35908751 115908751 Oxidation PF HQ PF HQ PF HQ PF HQ PF HQ PF HQ

Error Rate Oxidation Aligned Aligned Aligned Q20 Aligned Q20 Aligned Aligned

Organism OXO Q OXO Bases AP Bases Bases AP 3¾ases Reads AP Reads

253 Human 0 76.09059 3382941433 3382941433 3317335789 3337335789 44906483 44906481

254 Human 0.00148 28.28827 4217193129 4217393129 3991890897 3993 890897 57668320 57668320

255 Human 9.00E-05 40,41848 8638867456 8638867456 8486088012 8486088012 116579901 116579901

256 Human * 9.66E-05 40,69708 9687598462 ' %8^:7598462 9520702140 9520702140 130677858 130677858

257 Human 0 75.50176 3178554092 ' 3178554092 31 37440820 3117440820 42361041 42161041

258 Human 5.00E-05 43.03943 908934597 ί ' 9089345973 8942658723 8942658723 123529299 121529299

259 Human 0 75.63993 3166744903 3166744903 3105715638 3105715638 43992952 41992952

260 Human 0.00015 38.17664 9940336558 9940316558 9775392634 9775392634 332816856 132836856

263 Human 1.00E-05 50.53683 1363 3572111 136115723 3 3 13478949368 13478949368 383049797 181049797

262 Human 2.00E-04 36.94151 2787293319 2787293319 27743 56739 2774156739 36942320 36942320

263 Human 0.00022 36.56872 2857866440 2857866440 2844762610 2844762630 37872588 37872588

264 Human 0.00026 35.89006 2887572751 2887572753 2873415933 2873415933 38265286 38265286

265 Human 0.00019 37.1733 2799339121 2799339121 2786850494 2786850494 37093564 37093564

266 Human 0.00019 37.22366 ' 2781947433 278Ϊ947433 ' 2769064008^" 2769064008 36855990 36855990

267 Human 0.00032 34.93291 ' 2964677272 2964677272 ' 2951093983 2951093981 39281110 39281110

268 Human 0.00019 37.29028 2745741664 2745741664 2733053734 2733053734 36398329 36398329

269 Human 3.00E-05 45.30382 14302268384 14302268184 14237282367 34237282167 189651 344 3 89651144

270 Human 3.00E-04 35.2067 6691450765 6693450765 6603951036 6603951016 890241 34 89024114

27 i Human t .OOE-05 51.1777 5910058085 5930058085 5827831824 5827831824 78395032 78395032

272 Human 0 78, 16998 6394088626 6394088626 6306606565 6306606565 84839656 84839656

273 Human 0.00012 39,38633 4728069662 4728069662 4662542008 4662542008 62772369 62772369

274 Humaii 6.00E-05 42,60846 6019802265 6019802265 5937526211 5937526211 79899199 79899199

275 Humaii 1.00E-04 39,8396 5254586481 5254586481 5180302782 5180302782 69794460 69794460

276 Human ' 0 77,98302 5907372469 ^ 5907372469 5825075347 5825075347 784Ϊ8875 78 18875

277 Human 2.00E-05 47.44178 15244030558 ' Ϊ5244030558 15378302934 ' 15178302934 203997630 201997630

278 Human 3.00E-05 45.9583 15641099084 15641099084 15570389451 15570389451 207379413 207379413

279 Human 2.00E-05 46.76907 5609283116 56092833 36 5532715189 5532715389 74476572 74476572

280 Human 3.00F.-05 45.36625 5273942785 5271942785 5397992354 5197992354 69948279 69948279

28 S Human 0.00025 36.01945 123 3 5538649 12115538649 12063108142 12063108342 360784668 160784668

282 Human i.OOE-04 39.93467 475323 2401 4753212403 4536694635 4536694635 65435107 65435107

283 Human 7.00E-05 41.27865 5634537847 5634537847 5423736921 5421736923 77044584 77044584

284 Human 3.00E-05 44.79818 6854643908 6854643908 6759955779 6759955779 90903329 90903329

285 Human 3.00E-05 45.60127 * 72865 Ϊ Ϊ 530 72865ΪΪ530 * 7184920879 7184920879 96735290 96735290

286 Human 0.00013 38.92349 ' 48614(36503 4863406503 ' 4587230793 4587230793 67620505 67620505

287 Human 8.00E-05 40.80112 ' 6100776392 6100776392 ' 6000876873 6000876873 82365754 82365754

288 Human 8.00E-05 40.81316 13371857630 13371857630 13168059629 13368059629 180909243 380909243

289 Human 9.00E-05 40.27885 5696494599 5696494599 5566184438 5566184438 77584838 77584838

290 Human 0.00015 38.13338 6083494675 6083494675 5983170702 5983170702 82300893 82300891

29 i Human 0.00019 37, 15117 13473854396 13473854396 13269856462 13269856462 182567808 382567808

292 Human 7.00E-05 43 ,72725 12362106162 12362306162 12046990344 12046990144 169114736 369114716

293 Human 0.00025 36,05157 6485526400 6485526400 6378574275 6378574275 87519904 87519904

294 Human 0 79,02018 6861107853 6861107853 6771410750 6771410750 91520255 91520255

295 Human * Ϊ.00Ε-05 49,50913 5858228902 ' 5858228902 5769477580 5769477580 78598769 78598769

296 Human 9.00E-05 40.52326 9622527412 ' 9622527412 95663 43778 9566143778 127718051 127718051

297 Human 7.00E-05 41.60683 4473937624 ' 4473937624 4455606494 4455606494 59393627 59193627

298 Human 6.00E-05 42.62597 9493278403 9491278403 9434463976 9434463976 125960266 125960266

299 Human 0.00018 37.3754 7056056122 7056056322 6977019986 6977019986 93680905 93680905

300 Human 0.00017 37.77033 7297439701 7297419703 7235792845 7215792845 96885688 96885688

30! Human 8.00E-05 41.13932 8103603531 8101603533 8032328671 8012328673 107476375 107476375

302 Human 0.00018 37.53803 7640243583 7640243583 7556740122 7556740322 103416515 10141653 5

303 Human 8.00E-05 41.04767 8515820723 8515820723 8421507165 8421507165 113023340 113023340

304 Human 9.00E-05 40.35484 7433860498 7433860498 7351683220 7351683220 98736198 98736198

305 Human 0.00017 37.83811 ' 7649254114 7649254114 ' 7565239626 7565239626 101566338 101566338

306 Human 2.00E-04 37.00709 ' 6885590893 6885590893 * 6805845733 6805845731 91419548 91419548

307 Human 2.00E-04 37.08189 7123062263 7123062261 7042434478 7042434478 94547367 94547367

308 Human 0.00021 36.78724 7551543535 7553 543535 7467710655 7467710655 100218532 300218512

309 Human t .OOE-05 49.67897 7876009044 7876009044 7789735536 7789735536 104479226 304479226

310 Human t .OOE-05 48.93265 8235141 323 8235341123 8146912796 8346912796 109240907 309240907

311 Human 1.00E-04 40,06165 7119868360 7119868360 7041299263 7043 299263 94488793 94488791

312 Human 0.00021 36,81195 7237249997 7237249997 7157556050 7357556050 96109860 96309860

313 Human 0.00022 36,55139 7550305844 7550305844 7466927538 7466927538 100256700 100256700

314 Human ' 6.00017 37,70838 6820682754 * 6820682754 6743738193 6743738193 90507)816 90500816

315 Human 0.00019 37.32548 6966873042 ' 6966873042 6887227178 6887227378 92457308 92457308 Oxidation PF HQ PF HQ PF HQ PF HQ PF HQ PF HQ

Error Rate Oxidation Aligned Aligned Aligned Q20 Aligned Q20 Aligned Aligned

Organism OXO Q OXO Bases AP Bases Bases AP Bases Reads AP Reads

316 Human 0.000) 9 37.26049 8668923520 8668923520 856987903 3 8569879011 115074600 ) ) 5074600

317 Human 8.00E-05 4) , 04017 7734524046 7734524046 7647896876 7647896876 102657525 ) 02657525

318 Human 6.00E-05 42,46954 7551448676 7551448676 7467924560 7467924560 100208960 100208960

319 Human ' 0.66024 36,22098 7324155558 * 7324155558 7241666310 7241666310 9728Ϊ038 97281038

320 Human 6.00E-05 42.18839 8303 122016 ' 830 ί 122016 8207933821 8207933821 3 30217766 110237766

321 Human 2.00E-05 46.89148 7265886216 ' 7265886216 7385656039 7185650039 96382024 96382024

322 Human 0.00015 38.24362 7036183463 7036183463 6958621080 6958623080 93413508 93413508

323 Human 2.00E-04 36.90834 7554599003 7554599003 7469308941 7469108943 300276439 100276439

324 Human 2.00E-04 36.93453 7320275615 7320275635 7239344202 7239344202 97364624 97164624

325 Human 4.00E-05 44.51344 8397268231 8397268233 8304426054 8304426054 1 3 3438687 111438687

326 Human 0.00013 38.77898 6548022445 6548022445 6474814139 6474814339 86920259 86920259

327 Human 0.00017 37.7187) 7487542136 7487542336 7404567264 7404567264 99422216 99422236

328 Human 0.00017 37.73946 7626813901 7626813901 7543437755 7543437755 101240803 101240803

329 Human 2.00E-04 37. ^"10516 ' 7447645737 7447645737 ' 73647Ϊ6239 7364716239 98873363 98873363

330 Human 0.00016 38.0336 ' 6966511463 696653 Ϊ46 * 6888044029 6888044029 92463882 92463882

33 i Human 0.00016 37.9679 7220824355 7220824355 7139476443 7339476443 95869620 95869620

332 Human 0.000 i 3 38.79193 7220303062 7220303062 7140268363 7340268361 95832202 95832202

333 Human i .OOE-05 49.30042 8569674470 8569674470 8475416469 84754) 6469 113652657 3 J 3652657

334 Human 3.00E-05 45.90405 7483013039 748303 3039 7402846668 7402846668 99249688 99249688

335 Human 2.00E-04 37.05955 7574352322 7574352322 7491854633 7493 854613 100537353 300537351

336 Human 0.000) 9 37.23131 7879303064 7879303064 7789997993 7789997993 104595538 304595518

337 Human 0.00018 37,42338 7658053660 7658053660 7573283590 7573283590 101703972 101703972

338 Human 0.00018 37,41363 7032814373 7032814373 6954516504 6954516504 93333787 93333787

339 Human ' 6.660Γ9 37, 12705 7258836607 * 7258830607 7178947279 7178947279 96350767 96350767

340 Human 2.00E-04 37.02839 7878510141 ' 7878510143 7790767967 7790767967 304597276 104597276

341 Human i.OOE-05 53.39934 8906228338 8906228338 8809707143 8809707343 3 38705186 118705386

342 Human 0.00021 36.8552 7083474724 7083474724 7004747182 7004747382 9408) 089 94083089

343 Human 2.00F.-04 37.01705 8300493062 8300493062 8207441424 8207443424 3 30297643 110297643

344 Human 7.00F.-05 41.4222 7832) 30519 7812130539 7727790380 7727790380 303658635 103658635

345 Human 0.00014 38.47848 763 ) 832044 7631832044 7546996898 7546996898 103342813 101342833

346 Human 0.00019 37.11633 676) 652997 6761652997 6685811861 6685811863 89774542 89774542

347 Human 0.00022 36.61274 8470746800 8470746800 8376254079 8376254079 112470321 112470321

348 Human 0.00021 36.82802 ' 755739Ϊ822 755739Ϊ822 ' 7474270181 7474270181 100297392 100297392

349 Human 4.00E-05 44.55671 ' 7954826883 7954826881^" ' 7868390485 7868390485 105520632 305520632

350 Human 0.00023 36.38271 ' 7354727023 7354727023 ' 7273789877 7273789877 97591388 97591388

351 Human 0.00022 36.58708 8232218634 8232218634 8141937923 8341937923 109315233 309315233

352 Human 0.0002) 36.70971 7819109490 7839309490 7731921 3 34 7733921 114 103807085 303807085

353 Human 3.00E-05 44.79355 74126623 3 3 7432662111 7330340323 7330340123 98416082 984) 6082

354 Human 0.000) 9 37.23319 7153223887 7153223887 7073811349 7073811349 94938527 94938527

355 Human 0.0002) 36.88665 7901348879 7903348879 7814473340 78) 4473340 104889533 ) 04889531

356 Human 3.00E-05 45.89013 7119186545 7119386545 7038564780 7038564780 94530013 94530013

357 Human 2.00E-05 46,25815 7998168065 7998168065 7909257968 7909257968 106134047 106134047

358 Human ' 0.00021 36,7307 8182596869 * 8182590869 809253Ϊ195 8092531195 108633954 108633954

359 Human 0.00019 37.29503 7268803060 ' 7268803060 7385766329 7185700329 96547367 96547367

360 Human 5.00E-05 43.1123 3 8037567659 ' 8037567659 7948940919 7948940939 306678245 106678245

361 Human 2.00E-05 46.1437 7430827801 7430827803 7347678937 7347678937 98615093 98615093

362 Human 0.00017 37.78239 6489837686 6489837686 6436022692 6416022692 86367650 86167650

363 Human 0.00019 37.13505 73637) 5797 7361715797 7280956414 7280956434 97673950 97673950

364 Human 7.00E-05 41.34702 7248667820 7248667820 7165737332 7165737332 96223607 96223607

365 Human 2.00E-05 48.13863 7602802396 7602802396 7538332663 7518332663 100919104 100919) 04

366 Human 0.00021 36.74399 8134853129 8134853129 8044492897 8044492897 107985436 107985436

367 Human 2.00E-04 36.99807 7388219429 7388219429 7304518692 7304518692 98104235 98104235

368 Human 0.00015 38.36924 ' 5972057102 5972057102 ' 5916083449 5916083449 79416531 79416531

369 Human 0.00015 38.32225 * 5803854897 5803854897 * 5747414116 5747414116 77124776 77124776

370 Human 4.00E-05 43.78643 4586398133 4586398131 4542495309 4542495109 60863358 60863358

371 Human 2.00E-05 47.67573 4806666393 4806666393 4759046532 4759046532 63831623 63831623

372 Human 0.000) ) 39.56073 5510140629 5530340629 5455029005 5455029005 73226634 73226634

373 Human 0 55.65473 4058345300 4058345100 4019776376 4039776176 53876409 53876409

374 Human 0.000) 6 38.08112 4662115796 46623 3 5796 4617150725 4637150725 61915642 6) 915642

375 Human 0.000) 4 38.50687 6295674010 6295674010 623474583 3 6234745811 83655333 83655333

376 Human 0.00016 37,98152 4838232662 4838232662 4790369755 4790369755 64269196 64269196

377 Human ' 6.66022 36,52203 5115545307 *^" 5115545307 5066215718 5066215718 67930016 67930016

378 Human 6.00E-05 42.20687 4308596428 ' 4308596428 4266234225 4266234225 57219749 57219749 Oxidation PF HQ PF HQ PF HQ PF HQ PF HQ PF HQ

Error Rate Oxidation Aligned Aligned Aligned Q20 Aligned Q20 Aligned Aligned

Organism OXO Q OXO Bases AP Bases Bases AP Bases Reads AP Reads

379 Human 0.0001 5 38.22625 5216295495 5216295495 5165025955 5365025955 69264820 69264820

380 Human 2.00E-04 37.07254 4318278627 4318278627 4277398958 4277398958 57342897 57342897

381 Human 0.00012 39,3693 4832083076 4832083076 4787433047 4787433047 64209075 64209075

382 Human ' 6.00017 37,60799 3616658043 ' 3616658043 358787Ϊ304 3587871304 48Ϊ5Ϊ622 48151622

383 Human 0.00019 37.28198 4397377255 ' 4397177255 4355565792 4355565792 58377082 58377082

384 Human 0.00017 37.7882 5080664179 ' 5080664179 5033498348 5031498348 67464179 67464179

385 Human 0.00018 37.55643 5353687761 5351687763 5297158563 5297158563 73 3 16247 71116247

386 Human i.OOE-04 40.08282 5312019574 5312019574 5258593606 5258593606 70570859 70570859

387 Human 7.00E-05 41.85633 4984624425 4984624425 4937007360 4937007360 66394568 66194568

3S8 Human i.OOE-05 51.15637 4999743221 4999743223 4952227578 4952227578 66391474 66391474

389 Human 0.00011 39.60792 4007681389 4007681389 3975518375 3975518375 53521401 53521403

390 Human 9.00E-05 40.50728 4774862594 4774862594 4730249434 4730249434 63371809 63371809

39 ϊ Human 0.00015 38.32603 5306472921 5306472921 5257234897 5257234897 70660420 70660420

392 Human 0.00016 37.912 ' 4958678335 4958678335 ' 4910046249 4910046249 65865208 65865208

393 Human 0.00017 37.59102 ' 4750953499 4750953499 ' 4705906646 4705906646 63100754 63100754

394 Human 2.00E-05 47.10446 4842751088 4842751088 4793927559 4793927559 64311824 64311824

395 Human 0.00014 38.47461 4226915914 422691 5914 4186997638 4386997618 56166630 56166610

396 Human 0.00012 39.1384 5371901993 5373901991 5320013553 5320013553 71351070 73351070

397 Human 4.00E-05 43.66685 4972346536 4972346516 4925511446 4925511446 66028570 66028570

398 Human 1.00E-04 40.13303 4706716175 4706736175 4660715237 4660715217 62523720 62523720

399 Human 0.00017 37.65997 5096175095 5096375095 5047245633 5047245613 67841988 67841988

400 Human 0.00017 37,65562 5821351095 5821351095 5766429568 5766429568 77423658 77423658

401 Human 0.00018 37,56705 5762591894 5762591894 5707168826 5707168826 76603555 76603555

402 Human ' 0.66018 37,36316 5335ΪΪ9277 ' 5335119277 5281594391 5281594391 70873288 70873288

403 Human 8.00E-05 40.73693 5044380317 ' 5044180317 4995652984 4995652984 66963174 66963174

404 Human 5.00E-05 42.7013 4468256812 4468256812 4426986334 4426986334 59304247 59304247

405 Human 0.00017 37.72142 5308065838 5108065838 50576781 15 50576783 3 5 67851726 67853726

406 Human 0.00013 39.03938 4784187790 4784187790 4737702591 4737702593 63526699 63526699

407 Human 0.00015 38.27479 6249334393 6249314393 6392576038 6192576038 83006604 83006604

408 Human 0.00016 37.88266 4463633315 4463633315 4422444771 4422444773 59250192 59250192

409 Human 0.00017 37.76975 5036425474 5036425474 4986574639 4986574639 66890594 66890594

410 Human 0.00019 37.17227 4162315424 4162315424 4123518346 4123518346 55262735 55262735

41 ϊ Human 7.00E-05 41.82202 ' 462887368 Ϊ 4628873681^" * 4584954530 4584954530 61472060 61472060

412 Human 0.00024 36.27357 ' 3975085210 3975085210 ' 3936296472 3936296472 52819098 52819098

413 Human 4.00E-05 44.56932 ' 4182398106 4182398106 ' 4143908772 4343908772 55495958 55495958

414 Human 0.00015 38.14311 4876458498 4876458498 4829015303 4829015303 64791790 64791790

415 Human 0.00013 38.74887 4146232635 4346232635 4105493979 4305493979 55057427 55057427

416 Human 0.00017 37.70105 6224179422 6224379422 6162305644 6362305644 82778833 82778831

417 Human 0.00019 37.28832 4880711223 488073 1223 4832250943 4832250943 64835656 64835656

418 Human 0.00012 39.35003 5003736452 5003736452 4954733978 4954733978 66439955 66439955

419 Human 7.00E-05 41 ,4449 4481764093 4483764093 4438561676 4438561676 59491028 59491028

420 Human 6.00E-05 42,31788 4749785613 4749785613 4701892601 4701892601 63096893 63096893

421 Human ' 6.00013 38,82435 5033574515 ' 5033574515 4984853828 4984853828 66834Ϊ29 66834129

422 Human 7.00E-05 41.821 3 3 411 3232877 ' 4111232877 4072224870 4072224870 54576475 54576475

423 Human 0.00015 38.28039 5159834027 ' 5159834027 51 32250861 5112250861 68640352 68640352

424 Human 9.00E-05 40.591 35 5038380595 5038380595 4988589635 4988589635 66911356 66911356

425 Human 0.00018 37.3834 5348048273 5148048273 5097844477 5097844477 68397659 68397659

426 Human 0.00018 37.47707 6229320400 6229320400 6368866241 6168866241 82878707 82878707

427 Human 8.00E-05 40.93348 4805823014 4805823014 4757548723 4757548723 63850915 6385093 5

428 Human 8.00E-05 40.90532 4680820165 4680820165 4635020684 4635020684 62394623 62194623

429 Human 0.00012 39.16034 4808253122 4808253122 4760987728 4760987728 63884713 63884713

430 Human 2.00E-05 47.49866 4717870784 4717870784 4673089418 4673089418 62642606 62642606

431 Human 3.00E-05 45.0036 ' 3599472030 3599472030 ' 3565517262 3565517262 47780695 47780695

432 Human 0.00011 39.50087 * 4807605491 4807605491 ' 4761077282 4761077282 63840586 63840586

433 Human 0.00016 37.98014 4716852063 4716852063 4670339823 4670339823 62658163 62658161

434 Human 6.00E-05 42.13817 4603435394 4603435394 4559016226 4559016226 61110980 61 3 10980

435 Human 9.00E-05 40.65124 5385909299 5385909299 5332888950 5332888950 71520103 71520103

436 Human 0.00012 39.25204 4967180570 4967380570 4917784986 4937784986 65990763 65990763

437 Human 9.00E-05 40,3199 4695230447 4695230447 4651346520 4653 346520 62343900 62343900

438 Human 4.00E-05 43,92284 4521064439 4523064439 4478061564 4478061564 60028893 60028891

439 Human 0.00014 38,47654 4667933569 4667933569 4623885631 4623885631 61966751 61966751

440 Human ' 6.66015 38,23038 4513257376 ' 4513257376 4469590463 4469590463 59934055 59934055

441 Human 0.00022 36.56392 4202379908 ' 4202379908 4163437445 4163437445 55798990 55798990 Oxidation PF HQ PF HQ PF HQ PF HQ PF HQ PF HQ

Error Rate Oxidation Aligned Aligned Aligned Q20 Aligned Q20 Aligned Aligned

Organism OXO Q OXO Bases AP Bases Bases AP 3¾ases Reads AP Reads

442 Human 0.000) 2 39.35251 4924212481 492423 2481 4876561047 4876561047 65369643 65369643

443 Human 7.00E-05 4) , 73854 5121728289 5123728289 5072497203 5072497201 68030714 68030714

444 Human 3.00E-05 45,34981 5117646286 5117646286 5068367067 5068367067 67956912 67956912

443 Human ' 3.00E-05 45,76392 4248812451 ' 4248812451 4209900914 4209900914 56396680 56396680

446 Human 3.00E-05 45.52893 4646348960 ' 4646348960 4602447861^" 4602447861 63678358 61678358

447 Human 0.00012 39.4014 4139791487 ' 4139791487 4100446340 4100446340 54959957 54959957

448 Human 0.00016 38.08802 4723662583 4721662583 4675907924 4675907924 62844110 628441 30

449 Human 0.00019 37.33675 4963034657 4961034657 493402.3977 4914023977 65848822 65848822

450 Human 7.00E-05 41.61027 4477562.213 4477562233 4435694799 4435694799 59425557 59425557

45 ϊ Human 7.00E-05 41.80387 5136232973 5136232973 5086699321 5086699323 68236953 68216953

452 Human 5.00E-05 43.12023 4177490102 4177490102 4138495432 4138495432 55471696 55471696

453 Human i.OOE-05 51.32375 5433425994 5433425994 5382511960 5382511960 723 3 8849 72118849

454 Human 8.00E-05 41.10071 4908632874 4908632874 4860805724 4860805724 65191930 65191930

455 Human 0.00014 38.50051 ' 4778403015 4778403015 ' 473Ϊ525722 4731525722 63468157 63468157

456 Human 0.00018 37.57494 ' 4712863598 4712863598 ' 466708Ϊ740 4667081740 62582313 62582313

457 Human 0.00014 38.6361 4892999688 4892999688 4845149962 4845149962 65002603 65002601

458 Human t .OOE-04 40.17362 4815138586 4835338586 4770199999 4770199999 63922582 6392.2582

459 Human t .OOE-04 39.93775 4767158373 4767358171 4720489006 4720489006 63320183 6332.0181

460 Human 8.00E-05 40.7881 5486021925 5486021925 5432543245 5432543245 72877963 72877961

46 i Human 0.00019 37.11873 5116268752 5116268752 5067405146 5067405146 67936365 67936365

462 Human 2.00E-05 47.546 12870444878 12870444878 12764652083 12764652081 172400028 372400028

463 Humaii 0 80,38945 11655944832 11655944832 11556202119 11556202119 155165791 155165791

464 Humaii 0.00014 38,66118 11569741914 11569741914 11464385879 11464385879 154320637 154320637

465 Human ' 2.66E-05 47,98336 14570045502 ' Ϊ4570045502 14456136619 ' 14456136619 193980775 193980775

466 Human l.OOE-05 49.74468 11564968256 ' Π564968256 Ϊ 1464962555 ' 11464962555 154120363 154120363

467 Human 4.00E-05 44.32752 9667482921 9667482923 9583069743 9581069743 128859676 128859676

468 Human 3.00E-05 44.71 166 1 3984240830 11984240830 1 3882862074 1 1882862074 359638918 159638938

469 Human 2.00E-05 48.0588 1 33373 70093 11337170093 1 3234778839 1 1234778839 353 3 70889 151170889

470 Human 7.00F.-05 41.37838 12393315865 12393 15865 122852.15622 12285235622. 365342.707 165342707

47 ϊ Human 0 57.99165 12232657024 12212657024 12308319664 12108319664 162760795 162760795

472 Human i .OOE-05 48.69343 12323426312 12323426332 12223 580425 12221580425 164067455 164067455

473 Human 2.00E-05 46.18344 11581866911 11581866911 11482854730 11482854730 154369347 154369347

474 Human 6.00E-05 42.52136 * 17)827631366 10827631366 ' 17)734305449 10734305449 144295642 144295642

475 Human 4.00E-05 44.17153 * ^"l()83i)i 86299 Ϊ0830Ϊ86299 ' 10736632795 10736632795 1442961 33 344296113

476 Human 0 80.77403 ^ Ϊ2087875666 12087875666 ^ 11985056347 1 3985056347 161018166 361018166

477 Human 0 79.20919 9217509899 9217509899 9138870522 9338870522 122712853 322712851

478 Human 9.00E-05 40.71927 10829156534 108293 56534 10735226358 307352.26358 144333808 344333808

479 Human 0 80.55844 11439587207 1 3439587207 11330778584 3 3330778584 152662965 3 52662965

480 Human 8.00E-05 4) , 12621 13196019126 13196019126 13080729699 13080729699 175874230 375874230

48 i Human 5.00E-05 43, 13308 9878983193 9878983191 9792106426 9792106426 131621833 333621833

482 Human 1.00E-04 40, 13691 9598013677 959803 3677 9512497523 9532497521 127948320 327948320

483 Human 0.00012 39,06419 12703929383 12703929383 12593480938 12593480938 169324456 169324456

484 Human ' 3.00E-05 44,73135 10565707145 ^ 17)565707145 10474058018 ' 10474058018 140808286 140808286

485 Human 2.00E-05 46.92305 8224962969 * 8224962969 8155047385 8155047385 109576672 109576672

486 Human l.OOE-04 40.02312 11838977072 ' 11818977072 1173 3948642 ' 11711948642 157604028 157604028

487 Human 0 57.97299 8457963807 8457963807 8304056872 8304056872 1 33083572 113083572

488 Human 0.00011 39.78182 1 3236247188 11216247388 1 3 3 3 5968592 1 1115968592. 349567761 149567763

489 Human l.OOE-04 39.85323 12336278372 12136278372 12033157136 12033157336 363673406 161673406

490 Human 0.00011 39.6743 10935093227 10935093227 10842294607 10842294607 145759234 145759234

49 ϊ Human 0.00012 39.31437 10973768252 10973768252 10882967888 10882967888 146390906 146190906

492 Human 0.00011 39.77294 12952198588 12952198588 12842751012 12842751012 172577874 172577874

493 Human l.OOE-04 39.8974 10238455069 10238455069 10148641439 10148641439 136467598 136467598

494 Human 0.00011 39.67083 ' Ϊ18990738Ϊ0 11899073810 ' 11801134784 11801134784 158431369 158431369

495 Human 0.00013 38.77843 ' 11699413969 i 1699413969 ' ϊί60ΐΎ0350ϊ 1 3601103501 155902605 355902605

496 Human 0.00013 38.99197 11947960743 11947960743 11835744048 1 3835744048 159559186 359559186

497 Human 0.0001 1 39.58619 12362827956 1236282.7956 12264862409 32264862409 164541678 364541678

498 Human 0.00013 38.85631 9591411065 959343 1065 9511592984 953 3 592984 127723360 3 27723160

499 Human 0.00012 39.14909 11077074747 1 3077074747 10975532223 30975532223 147779642 347779642

500 Human 0.000) 2 39.18388 13220612475 13220612475 13109261475 13309261475 176103250 376103250

50 i Human 0.000) 3 38.94903 11931003449 11933003449 11832046934 1 3832046934 158939523 3 58939521

502 Human 0.00012 39,36974 8052550155 8052550155 7985596712 7985596712 107251421 107251421

503 Human * Ϊ.00Ε-04 39,90579 10840433486 ' 17)840433486 10742197122 ' 10742197122 144585472 144585472

504 Human 2.00E-05 46.88778 7168574599 * 7168574599 7090486189 7090486389 95542846 95542846 Oxidation PF HQ PF HQ PF HQ PF HQ PF HQ PF HQ

Error Rate Oxidation Aligned Aligned Aligned Q20 Aligned Q20 Aligned Aligned

Organism OXO Q OXO Bases AP Bases Bases AP 3¾ases Reads AP Reads

505 Human 2.00E-05 46.12453 6442960732 6442960732 6372141764 6372141764 85860917 85860917

506 Human 1.00E-04 40.03112 6101790450 6103790450 6034022966 6034022966 81334020 83334020

507 Human 3.00E-05 46,05174 6429250521 6429250521 6361659570 6361659570 85593545 85593545

508 Human ' 0 79,56213 6978756811^" ' 697875681 Ϊ 6897509257 6897509257 93278994 93278994

509 Human 0.00013 38.94863 566920Ϊ799 ' 5669201799 560749Ϊ943 5607491943 75582154 75582354

510 Human 0.00012 39.32152 7083928390 ' 7083928390^" 7008965726 7008965726 94437266 94437266

511 Human 0.00011 39.50968 6493709601 6493709603 6420392641 6420392641 86638200 86638200

512 Human 1.00E-04 40.16204 6330339520 6330339520 6260685159 6260685359 84379068 84379068

513 Human 8.00E-05 40.79579 6314000991 6314000993 6245591276 6245593276 843 24131 84124333

514 Human 4.00E-05 43.66328 6350291946 6350291946 6283744804 6281744804 84634128 84614128

515 Human 5.00E-05 42.74405 6624256885 6624256885 6553204581 6553204583 88249959 88249959

516 Human 2.00E-05 46.37396 62541 1 2132 6254112132 6186986113 61869863 33 83320440 83320440

517 Human 5.00E-05 42.97992 6392303878 6392303878 6323844888 6323844888 85301668 85301668

518 Human 0.00012 39.24633 ' 6555400713 6555400713 ' 64860056Ϊ7 6486005617 87373146 87373146

519 Human 0.00011 39.53912 ^" 7158785896 7158785896 * 7081984513 7081984513 95747802 95747802

520 Human 1.00E-04 40.19815 7069604953 7069604951 6994216093 6994216091 94227355 94227355

521 Human 7.00E-05 41.51711 7080722970 7080722.970 6998291945 6998291945 94460863 94460861

522 Human 0.00013 39.03138 6582431092 6582431092 6508777030 6508777010 87768896 87768896

52.3 Human 0 78.2.6107 6203553972 6203553972 6135033362 6335033362 82652455 82652455

524 Human 8.00E-05 40,91299 7533829757 7533829757 7452423145 7452423145 100663623 300663621

525 Human 0.00043 33,66943 6501768759 6503768759 6435865133 6435865133 86688585 86688585

526 Humaii 0 78,58863 6446530835 6446530835 6378070552 6378070552 85900609 85900609

527 Humaii 0 76,22451 7711477468 7711477468 7641252263 7641252263 103367291 103367291

528 Human * 8.66E-05 41, 11403 7792673283 ' 7792073283 7708498125 7708498125 104022614 104022614

529 Human 4.00E-05 44.27788 7350019838 ' 7350019838 7275815521 7275815521 97904479 97904479

530 Human l.OOE-05 49.18445 8657293429 8657293429 8560622438 8560622438 1 36031170 116031 370

531 Human 0 78.38238 5485063934 5485063934 5422785742 5422785742 73396460 73196460

532 Human 1.00E-05 51.39469 8058681444 8058681444 7979295589 7979295589 307443414 107443434

533 Human 3.00E-05 45.70174 7933673798 7931673798 7706970678 7706970678 308842212 108842232

534 Human 4.00E-05 44.25309 7110201265 7Π0201265 7036562067 7036562067 94801367 94801367

535 Human 3.00E-05 45.55064 5969258179 5969258179 59053 82940 5905182940 79555127 79555127

536 Human 0 78.24021 6278881052 6278881052 6210983429 6210983429 83656299 83656299

537 Human 0.00144 28.43135 ^" 7192517470^" 7192517470 ' 7Π7428138 7117428138 95983689 95983689

538 Human 5.00E-05 42.84898 ' 6141103526 6143 103526 ' 6069646247 6069646247 81951825 81951825

539 Human 0 54.94396 ' 15318663981 15338663981 ' ^"15246160948 15246160948 202763748 202763748

540 Human 0 81.69495 16243880907 16243880907 16169428204 16369428204 215006325 215006325

541 Human 0.00012 39.10208 11095879676 1 3095879676 11057299748 3 3057299748 147070742 347070742

542 Human 0.00013 39.02.626 6518738077 6538738077 6493885253 6493885253 86339053 86339053

543 Human 0.00025 36,0178 10728977385 10728977385 10686933826 10686933826 142263024 342263024

544 Human S.00E-05 41 ,27564 8975996235 8975996235 8916492907 8936492907 119264053 3 39264051

545 Human 0.00013 38,82216 10159698850 10159698850 10091669040 10091669040 135060134 335060134

546 Human 0 79,97807 9627780304 9627780304 9562495296 9562495296 127930387 127930387

547 Human ' 0.66012 39, 15525 8955286312 ' 8955286312 8897245604 8897245604 1 Ϊ8963066 118963066

548 Human 0.00019 37.32738 8755640091 ' 8755640093 8698032324 8698032324 3 36346507 116346507

5 9 Human 0.00011 39.65298 9130363430 ' 9130363430^" 9073020903^" 9071020903 323311979 121313979

550 Human 0.00015 38.23844 7586106726 7586106726 7535078083 7535078083 100861137 100861 337

551 Human 0.00015 38.17777 6689464992 6689464992 6644070341 6644070343 88940989 88940989

552 Human 0.00012 39.39562 8616378071 8616178073 8560366840 8560366840 3 34507594 114507594

553 Human 0.00014 38.41523 7388676620 7388676620 7339422788 7339422788 98233946 98233946

554 Human 0.00013 38.99618 10126432145 10126432145 10056088783 10056088783 135604602 135604602

555 Human 3.00E-05 45.27097 6929575237 6929575237 6741265295 6741265295 96014565 96014565

556 Human 2.00E-05 47.89886 9592993733 9592993733 9529182156 9529182156 127458555 127458555

557 Human 0 81.52048 * 8737233549 8737233549 ' 8484315203 8484515203 118925339 118925339

558 Human 2.00E-05 46.14417 ' 8829837878 8829837878 ' 876795Ϊ533 8767951513 118490520 3 18490520

559 Human 0.00011 39.74546 7742535295 7742535295 7690195180 7690195180 102893520 302893520

560 Human 0.00013 38.76926 8837675550 8837675550 8776646423 8776646423 117533733 3 37533731

561 Human 0.00012 39.18273 6483396456 6483396456 6438338347 6438338147 86204700 86204700

562 Human 0.00012 39.32.386 8598202327 8598202.127 8540457099 8540457099 1 14362238 3 34362218

563 Human 0.00012 39,22635 8295552353 8295552351 8240975987 8240975987 110241234 3 30241234

564 Human 0.00013 38,9273 8424164323 8424364323 8368081102 8368081102 112031493 3 32031493

565 Human 0 75,02207 12429926586 12429926586 12317432974 12317432974 165888987 165888987

566 Human ' 6 74,9914 14173733598 ' Ϊ4Ϊ73733598 Ϊ 4049648318 ' 14049648318 190048883 190048883

567 Human 2.00E-05 48.1112 14303899736 ' Ϊ4303899736 Ϊ4376232937 ' 14176232937 193835548 191835548 Oxidation PF HQ PF HQ PF HQ PF HQ PF HQ PF HQ

Error Rate Oxidation Aligned Aligned Aligned Q20 Aligned Q20 Aligned Aligned

Organism OXO Q OXO Bases AP Bases Bases AP 3¾ases Reads AP Reads

568 Human 0 78.5072 14319892834 14339892834 14174184033 14374184031 191395876 393 395876

569 Human 0 80.65133 13398956225 13398956225 13258183562 13258183562 178890172 378890172

570 Human 0 73,25996 13632029959 13632029959 13493350573 13493350573 183481678 183481678

571 Human * 7.66E-05 41,50948 10332023554 ' Ϊ0332023554 Ϊ023 ΪΪ9993 ' 10234119993 137727236 137727236

572 Human 7.00E-05 41.59743 10785186219 ' Ϊ0785Ϊ86239 10671547712 ' 10671547712 143981243 143981243

573 Human 0 70.23392 12557552268 12557552268 12420711398 ' 1242071 3398 169244629 169244629

574 Human 0 80.28279 13773804593 13773804593 13656310702 13656310702 183397905 183397905

575 Human 0 75.85473 15177327247 15177327247 15038452762 15038452762 202676254 202676254

576 Human 0 79.35425 9493248088 9493248088 9382700472 9382700472 326853746 126853746

577 Human 5.00E-05 43.2925 10290755985 10290755985 10393427808 10193427808 137398811 13719883 3

578 Human 7.00E-05 41.80352 10379665479 10379665479 10275980044 10275980044 138477742 138477742

579 Human 0 76.15044 14451 525137 14451525137 14332021904 14312023904 193752956 193752956

580 Human 2.00E-05 46.92499 16105957117 16105957117 15954988653 15954988653 215627529 215627529

581 Human 0 78.5Ϊ903 * 7270894198 7270894198 ^ 7187113565 7187113565 97029139 97029139

582 Human 0.00013 38.88308 ' 9635290793 9635290791 ' 9511978606 953 1978606 128823643 328823641

583 Human 1.00E-04 39.81881 9191888375 9193888375 9079806860 9079806860 122728475 322728475

584 Human 0.00019 37.16127 7453816097 7453836097 7364989033 7364989013 99543767 99543767

585 Human 7.00E-05 41.80211 11472228922 1 3472228922 11332544243 3 3332544243 153283550 3 53283550

586 Human 0.00025 36.02426 9387963676 9387963676 9264857330 9264857130 125598845 3 25598845

587 Human 0.00014 38,45223 8127990683 8127990681 8020053230 8020053210 108758758 308758758

588 Human 0.0001 1 39,66023 9516546760 9516546760 9396084785 9396084785 127203634 327203614

589 Humaii 4.00E-05 43,63989 8843978715 8843978715 8724109214 8724109214 118332865 118332865

590 Humaii 0.00017 37,77186 7567746368 7567746368 7479026058 7479026058 101065096 101065096

591 Human ' 0 78, 17969 11574531970 ' Ϊ1574531970 Ϊ 1456297392 ' 11456297392 154278324 154278324

592 Human 3.00E-05 44.67549 9730371691 ' 973037Ϊ693 9605634969 9605634969 130343480 130343480

593 Human 6.00E-05 42.0318 13530056843 13510056843 13339757295 13339757295 183203257 181203257

594 Human 0 57.81886 1 1657729634 11657729634 1 3524689897 1 1524689897 355630587 155630587

595 Human 0 79.3012 13734353002 13714353002 13552361460 13552363460 3853 28604 185128604

596 Human 0 77.69988 15274783686 15274783686 15092912667 15092932667 207311942 20733 3942

597 Human 0.00012 39.0901 8649830540 8649810540 8543307381 8543307383 1 35583245 115583245

598 Human i.OOE-05 48.90074 9690846373 9690846373 9589201449 9589201449 129436768 129436768

599 Human 0 61.2281 12586014552 12586014552 12438441891 12438441891 169041913 169041913

600 Human 8.00E-05 41.20152 * 11211341686 11211341686 ' Ϊ10824938Ϊ3 11082493813 149969885 149969885

60 i Human 5.00E-05 42.67313 ' Ϊ3622958338 13622958338 ' Ϊ3453850528 13453850528 183188369 383188369

602 Human 4.00E-05 43.59932 ' 9735760763 9735760763 ' 9625921142 9625921142 130336763 330336763

603 Human 1.00E-05 48.79225 12389836304 12389836304 12227449738 12227449738 167284583 367284581

604 Human 4.00E-05 44.56651 10375338258 10375338258 10265399436 30265399436 138993386 338993186

605 Human 3.00E-05 45.67533 9523392508 9523392508 9412672573 943 2672571 127645360 3 27645160

606 Human 5.00E-05 43,33225 10469814443 10469814443 10353498293 10353498293 140242035 340242015

607 Human 5.00E-05 43,26061 10884223150 10884223150 10754925586 10754925586 145857495 345857495

608 Human 2.00E-05 47,71134 8720461413 8720461413 8622546524 8622546524 116822903 3 36822903

609 Human 2.00E-05 47,24623 11784748013 11784748013 11663345220 11663345220 157318451 157318451

610 Human * 6.66E-05 42,52682 9484663254 ' 9484663254 9370079417 9370079417 127Ϊ65834 127165834

611 Human 4.00E-05 44.38323 Ϊ 16863 23799 ' 11686123799 Ϊ 1552368237 ' 11552368237 156473462 156473462

612 Human 5.00E-05 42.7564 10531219428 ' 10531219428 10433832014 ' 10413832014 140714052 140714052

613 Human 5.00E-05 43.34474 12523666370 12523666370 12381749357 12381749357 167597709 167597709

614 Human 7.00E-05 41.67858 12266030249 12266030249 12308006520 12108006520 365643658 165643658

615 Human 2.00E-05 47.87986 1 1756522722 11756522722 1 1630409596 1 1610409596 358089716 158089736

616 Human 3.00E-05 45.14477 9879695449 9879695449 9763942211 976394223 3 132097627 132097627

617 Human 4.00E-05 43.82405 8433560050 8433560050 8343297319 8341297339 1 33434666 113434666

618 Human 5.00E-05 42.96885 9203489515 9203489515 9080001462 9080001462 124996470 124996470

619 Human 3.00E-05 44.72769 11860218128 11860218128 11727379734 11727379734 158897965 158897965

620 Human 4.00E-05 43.76964 * 9824544232 9824544232 ' 9696612968 9696612968 131652735 131652735

621 Human 0 55.61683 ' Ϊ0649762449 Ϊ 0649762449 * Ϊ0525966565 10525966565 142095353 342095353

622 Human 1.00E-05 51.71356 9503190485 9503190485 9386646495 9386646495 126881102 326881102

623 Human 8.00E-05 40.9744 10056947005 10056947005 9927265234 9927265234 134467584 334467584

624 Human 0 80.01972 9692808820 9692808820 9570090707 9570090707 129566393 3 29566191

625 Human 8.00E-05 40.79551 8391445484 8393445484 8283371843 8283371843 1 12213407 3 32213407

626 Human 5.00E-05 42,93465 9542435472 9542435472 9419558076 9439558076 127570436 327570416

627 Human 5.00E-05 43,38192 7654728863 7654728863 7561794140 7563 794140 102319383 302319381

628 Human 8.00E-05 40,98339 10493359619 10493359619 10364587946 10364587946 140198730 140198730

629 Human ' 0.660 ii 39,61849 89470555)6 ' 8947055406 882Ϊ620420 8821620420 119749087 119749087

630 Human l.OOE-04 40.06493 9599509255 ' 9599509255 9479580272 9479580272 128289209 128289209 Oxidation PF HQ PF HQ PF HQ PF HQ PF HQ PF HQ

Error Rate Oxidation Aligned Aligned Aligned Q20 Aligned Q20 Aligned Aligned

Organism OXO Q OXO Bases AP Bases Bases AP Bases Reads AP Reads i Human 1.00E-04 40.09871 1096862778) 10968627781 10841032967 10841032967 146447082 3464470822 Human 0.000 i i 39.74368 10571271040 1057) 271040 10451663520 10451663520 141099203 3430992033 Human 6.00E-05 42,47691 10515964628 10515964628 10393489833 10393489833 140442032 1404420324 Human ' 0.600 ii 39,70344 8156869452 ' 8156869452 80628Ϊ9290 8062819290 108902704 1089027045 Human i.OOE-04 39.98949 6674967796 ' 6674967796 6592226504 6592226504 89211683 892116836 Human 0.00011 39.61632 9634046608 ' 9634046608 952987Ϊ982 9529871982 128559678 1285596787 Human 0 79.73138 10128823303 10128823303 10002760561 10002760561 135305127 1353053278 Human 2.00E-05 46.70696 7812919797 7812919797 76920) 0829 7692010829 105063806 1050638069 Human 0 79.76502 1 1878293146 11878293146 1 1746598284 11746598284 358609769 1586097690 Human 0 79.76448 10690382009 10690382009 10576431667 10576433667 142635816 142635836 i Human 0 78.94445 14448245029 14448245029 14288888148 14288888348 193415005 1934150052 Human 0 73.75776 14636387340 14636387340 14483865249 14483865249 195684375 1956843753 Human 5.00E-05 42.8448 10147779461 10147779461 10022832747 10022832747 135795747 1357957474 Human 2.00E-05 47.07148 ' Ϊ2845062740^" i 2845062740 ' ^"12675742680 12675742680 173277038 1732770385 Human 3.00E-05 45.50239 ' Γ3550Ϊ3683 Ϊ 13550) 36811^" ' Ϊ3383 Ϊ22655 13383122655 182214693 3822146936 Human 4.00E-05 44.17034 9312090353 9312090351 9214034278 9234034278 124948152 3249481527 Human 4.00E-05 44.46803 9533488098 9533488098 9428427442 9428427442 127524746 3 275247468 Human 3.00E-05 45.47111 23288216448 232882) 6448 23036697219 23036697219 312337729 3323377299 Human 4.00E-05 43.77332 9096980367 9096980367 8992778409 8992778409 122406598 3 224065980 Human 0.000) 2 39.1291 9691895812 9693895812 9579270972 9579270972 129404499 329404499 i Human 0.000) 3 38.79513 9656537323 9656537323 9531742120 9533 742120 129148933 3291489132 Humaii 3.00E-05 44,75171 13063166000 13063166000 12922266749 12922266749 174744235 1747442353 Humaii 0.00012 39, 1516 9318628224 9318628224 9208899153 9208899153 124412663 1244126634 Human ' 6.66028 35,56795 10099887567 ' Ϊ009 887567 9986356002 9986356002 13480Ϊ658 1348016585 Human 0.00012 39.35002 6763 ) 30391^" ' 6761130393 6720296703^" 6720296703 89840180 898401806 Human 0 53.49273 7678957125 7678957125 7629613432 7629613432 102040695 1020406957 Human 5.00E-05 43.30104 7104884906 7104884906 7059326599 7059326599 94480775 944807758 Human 0.00016 38.03238 8658566897 8658566897 8603374218 860337423 8 3 353 24770 1151247709 Human i.OOE-04 40.12048 804560) 420 8045601420 7993424694 7993424694 307075426 1070754260 Human 0.00016 37.96407 6195079026 6195079026 6154869205 6154869205 82384403 82384403! Human 0.00016 37.94728 9397829809 9397829809 9339) 02046 9339102046 125026976 1250269762 Human 2.00E-05 47.80396 7023016880 7023016880 6977569654 6977569654 93362624 933626243 Human 8.00E-05 41.03014 * 6299660730 6299660730 ' 62590606Ϊ6 6259060616 83765220 837652204 Human 1.00E-04 40.17415 ' 7467346632 7467346632 ' 7419835424 7439835424 99485378 994853785 Human 7.00E-05 41.66582 ' 7654401074 765440Ϊ074 ' 7604894169 7604894169 101956203 3019562016 Human 0.00011 39.70174 7064337243 7064337241 7019774403 7039774401 93916893 939168937 Human 0.000) 3 38.79233 6697265312 6697265312 6654903337 6654903337 89047887 890478878 Human 0.00013 39.02i3i 6347298433 6347298433 6306949544 6306949544 84508128 845081289 Human 0.000) 2 39.13163 1858138592) 1858) 385921 18459738025 18459738025 246906663 2469066630 Human 0.000) 7 37.59466 7676721820 7676721820 7627149188 7627149188 102189448 302189448 i Human 4.00E-05 44.60705 7389313180 73893) 3180 7339728934 7339728914 98396166 983961662 Human 8.00E-05 41,08945 6473867020 6473867020 6433000405 6433000405 86087922 860879223 Human ' 2.00E-05 47,87606 7657293662 ' 7657293602 7608183492 7608183492 101827555 1018275554 Human i.OOE-04 40.09553 7153776559 *^" 7153776559 7109168506 7109168506 95091480 950914805 Human 0.00012 39.1003 7616116194 ' 7616116194 7567770957 7567770957 103319464 1013194646 Human 2.00E-05 46.98533 6804525847 6804525847 6762159252 6762159252 90548154 905481547 Human 6.00F.-05 42.06689 5564289299 5564289299 55281 ) 5967 5528115967 74046727 740467278 Human 8.00F.-05 40.75758 7896955788 7896955788 78424) 8830 7842418830 305223137 1052233379 Human 0.00023 36.40796 7112086291 7112086293 7067550977 7067550977 94568642 945686420 Human 6.00E-05 42.48541 7147823881 7147823883 7102689945 7102689945 94992559 94992559 Ϊ Human 6.00E-05 42.02373 7523611135 7523611135 7476976008 7476976008 99959710 999597102 Human 0.00016 37.84443 7617480762 7617480762 7565926280 7565926280 101659705 1016597053 Human 0.00017 37.74757 ' 4769777097 4769777097 * 4739368857 4739368857 63393232 633932324 Human 4.00E-0S 44.46656 ' 5881740629 5883740629 ' 5844285354 5844285354 78160949 781609495 Human 1.00E-04 39.86497 8257405087 8257405087 8140584170 8340584170 110544264 3 105442646 Human 0.00013 38.78242 11003999226 1 1003999226 10843764725 30843764725 147364376 3473643767 Human t .OOE-04 40.03081 10704806740 10704806740 10545686333 30545686313 143427805 3434278058 Human 0.0001 ) 39.5) 554 11321606448 1 1321606448 11160742127 3 3 360742127 151524934 3 53 5249149 Human 0.000) 3 38.96878 10396604466 10396604466 10247245644 10247245644 139191553 3391915510 Human 0.000) 3 38.82337 8059039084 8059039084 7942555622 7942555622 107949054 3079490541 Human 0.00013 38,98969 10930171360 10930171360 10772270314 10772270314 146394650 1463946502 Human ' o.oooii 38,92347 9886Ϊ9Ϊ055 ' 9886191055 9739430567 9739430567 132440114 1324401143 Human 0.00014 38.60035 9329739909 * 9329739909 9193708200 9193708200 124945399 124945399 Oxidation PF HQ PF HQ PF HQ PF HQ PF HQ PF HQ

Error Rate Oxidation Aligned Aligned Aligned Q20 Aligned Q20 Aligned Aligned

Organism OXO Q OXO Bases AP Bases Bases AP Bases Reads AP Reads

694 Human 0.00012 39.07383 9629042035 9629042035 9488073223 9488073221 128920835 328920835

695 Human 0.00013 38.85227 9823379705 9823379705 9679774469 9679774469 131576654 333 576654

696 Human 0.00012 39, 18367 10598400207 10598400207 10443841344 10443841344 141933984 141933984

697 Human ' 0.660 ii 38,88106 10767921435 ' Ϊ0767921435 10609463203 ' 10609463203 I44229969 144229969

698 Human 0.00013 38.9852 7566175326 ' 7566175326 7456570308 7456570308 103330604 101330604

699 Human 0.00012 39.26023 9617323107 ' 9617323107 9480799688 9480799688 128801087 128801087

700 Human 0.00012 39.2063 7894976693 7894976693 7778119628 7778119628 105743417 105743417

70S Human 1.00E-05 53.20164 9034179291 9034179293 8940937545 8940937545 320349082 120149082

702 Human 0.00012 39.22231 1 1841662445 11841662445 1 3707740971 1 1707740971 357726198 157726398

703 Human 0 80.00551 10845108157 10845108157 1073 5671090 10715673090 144702024 144702024

704 Human 0 76.7126 14196494329 14196494329 13923 320895 13921320895 192780705 192780705

705 Human 2.00E-05 47.0S304 10951 1 12263 10951112263 10762198225 10762198225 1473 50240 147150240

706 Human 0 77.37563 10226423347 10226423347 10057094904 10057094904 139779587 139779587

707 Human 0 72.57808 ^" Ϊ419636684Ϊ 14196366841 ' Ϊ3878393370 13878393370 199688735 199688735

708 Human 0 76.14024 ' Ϊ2056433624 Ϊ2056433624 ^{" "}11813858760 1 3813858760 165890473 365890473

709 Human 0 58.53992 12386159005 12386159005 12138490353 12338490153 168699734 368699734

710 Human 0 75.99689 11997294017 1 1997294017 11762414487 3 3762414487 162576286 362576286

711 Human 7.00E-05 41.34694 8021376427 8023376427 7842693454 7842693454 107959386 307959386

712 Human 3.00E-05 45.49335 12464425193 12464425193 1226525943 5 32265259415 168282572 368282572

713 Human 0 79.08764 11218290333 11238290333 11017758367 1 303 7758367 151281854 3 53 281854

714 Human 5.00E-05 43.15328 7931574967 7933 574967 7798631838 7798631818 106533790 306533790

715 Humaii 9.00E-05 40,38167 10397959657 10397959657 10220046552 10220046552 139633750 139633750

716 Humaii 0.00013 38,96003 8655772090 8655772090 8494469314 8494469314 116592869 116592869

717 Human ^" 5.00E-05 42,84415 9820287612 * 9820287612 9640369333 9640309333 132166382 132166382

718 Human l.OOE-05 53.07136 8418396475 ' 8418396475 82673 287 io 8267128730 1 33144742 113144742

719 Human 0.00011 39.72565 8895595629 8895595629 8735863091 8735863091 1 39601090 119601090

720 Human 3.00E-05 45.00949 1 1316523271 11316523271 1 3 323075854 1 1121075854 352593225 152593225

721 Human 0.00014 38.63394 10107464091 10107464093 9924002954 9924002954 336025654 136025654

722 Human 7.00E-05 41.90381 10041811848 1004181 3848 9867215933 9867215933 335044218 135044238

723 Human 5.00E-05 42.98967 7604562684 7604562684 7545384017 7545384037 103 342936 101142936

724 Human l.OOE-05 51.09903 9498453317 9498453317 9423904023 9423904023 126301751 126301753

725 Human 5.00E-05 43.43292 9255722816 9255722816 9182308845 9182308845 123163776 123163776

726 Human 3.00E-05 46.07034 ' Ϊ0207694242 10207694242 ' ^"10132701466 10132701466 135789877 135789877

727 Human 0 79.51031 ' 9143033763 9143033763 * 9073654777 9073654777 121502827 321502827

728 Human 3.00E-05 46.02993 ' 6722439430 6722439430 ' 6669092653 6669092653 89438238 89438238

729 Human .00E-05 44.40265 9585597864 9585597864 9511652432 953 1652412 127467693 327467693

730 Human 6.00E-05 42.56027 9815565375 9835565375 9736317590 9736317590 130674473 330674473

731 Human 0 56.5666 8750371831 8750371831 8681739252 8683 739252 1 16438775 3 36438775

732 Human 9.00E-05 40.65348 9766813403 976683 3403 9693235234 9693235234 129862768 329862768

733 Human 9.00E-05 40.29536 9530952947 9530952947 9458084639 9458084639 126849924 326849924

734 Human 4.00E-05 43.88373 10187652363 10187652363 10114502339 103 34502319 135402966 335402966

735 Human 2.00E-05 46,99114 9668224935 9668224935 9586250787 9586250787 129896696 129896696

736 Human ' 6 78,35877 6911317595 ' 6911317595 68579Ϊ2397 6857912397 9Ϊ936409 91936409

737 Human 5.00E-05 42.848 8549107532 ' 85 Ϊ07532 84853 82718 8485182738 1 33658988 113658988

738 Human 7.00E-05 41.65679 9845874589 ' 9845874589 9770075660 9770075660 133060166 131060366

739 Human 5.00E-05 42.95729 9883536844 9881536844 9798528632 9798528632 133581025 131581025

740 Human 0.00011 39.52139 1 1260774121 11260774323 1 3 379855775 1 1179855775 349908519 149908539

741 Human 7.00F.-05 41.79069 9413161169 9413161 369 9343464868 9341464868 325237455 125237455

742 Human 0 79.88348 9748284947 9748284947 9676349956 9676149956 129597329 129597329

743 Human 3.00E-05 44.97648 9341 569504 9341569504 9268865542 9268865542 124235322 124235322

744 Human 0 78.92509 7829454700 7829454700 7769087022 7769087022 104036826 104036826

745 Human 7.00E-05 41.41009 7136928657 7136928657 7083521438 7083521438 94976905 94976905

746 Human 5.00E-05 42.69528 ^" 9975587600 9975587600 ' 9901581364 9901581364 132614308 132614308

747 Human 6.00E-05 42.32224 ' 8953651843 8953651841 ' 8888526303 8888526301 119022680 3 19022680

748 Human 4.00E-05 44.314 10110407531 101 30407531 10034516729 10034516729 134506705 334506705

749 Human 5.00E-05 42.78281 9249451384 9249451384 9180801523 9380801521 123110438 3 23110418

750 Human 0 79.40927 9276728264 9276728264 9205860996 9205860996 123386044 3 23386044

751 Human 0 78.62228 7329969584 7329969584 7274860367 7274860167 97405846 97405846

752 Human 6.00E-05 42.23678 8439942682 8439942682 8374635574 8374635574 112320938 3 32320938

753 Human 0 78.60889 7404272482 7404272482 7349281699 7349281699 98466183 98466183

754 Human 5.00E-05 42,96995 8816754746 8816754746 8749640472 8749640472 117361207 117361207

755 Human ' 6 71,30615 6450976763 ' 6450976763 6402243332 6402243332 85760458 85760458

756 Human 3.00E-05 46.03364 9153594399 ' 9153594399 9087458007 9087458007 123696017 121696017 Oxidation PF HQ PF HQ PF HQ PF HQ PF HQ PF HQ

Error Rate Oxidation Aligned Aligned Aligned Q20 Aligned Q20 Aligned Aligned

Organism OXO Q OXO Bases AP Bases Bases AP Bases Reads AP Reads

757 Human 0 78.72013 8001285816 8003285816 7939037707 7939037707 106454427 306454427

758 Human 2.00E-05 46.80208 9376277009 9376277009 9298986662 9298986662 124845038 324845038

759 Fiumaii 0 79, 11275 8218644020 8218644020 8155690692 8155690692 109286896 109286896

760 Fiumaii ' 3.00E-05 45,75603 8436486188 ' 8436486188 837Ϊ468456 8371468456 112193263 112193263

761 Human l.OOE-05 49.2832 8505434478 * 8505434478 8440Ϊ Ϊ3985 8440113985 1 33107897 113107897

762 Human 3.00E-05 44.96833 9337190362 ' 9337190362 9261786530 9261786530 124324746 124324746

763 Human 0 79.44686 9525100120 9525100120 9452906457 9452906457 126805662 126805662

764 Human 2.00E-05 46.43263 7397002017 7397002037 7336435859 7336435859 98567198 98567398

765 Human 0 78.81421 7297545234 7297545234 7242944451 7242944451 97032766 97032766

766 Human 6.00E-05 42.19356 6647076122 6647076322 65961 70369 6596170369 88485499 88485499

767 Human 0 79.49063 8750763704 8750763704 8683483754 8683483754 3 36397166 116397366

768 Human 5.00E-05 43.05892 9040652337 9040652337 8963407654 8963407654 320358423 120358423

769 Human 2.00E-05 47.33728 9230302194 9230302194 9161832793 9161832793 122706474 122706474

770 Human 0 79.40385 ' 8662620373 8662620373 * 8595149741 8595149741 115222178 115222178

77 i Human 0 79.86226 ' 9269728375 9269728375 ' 9197278647 9397278647 123365997 323365997

772 Human 0 79.39725 8493210936 8493210936 8428130830 8428130830 112916234 3 12916234

773 Human 0 78.74044 7961847747 7963 847747 7900209457 7900209457 105895608 305895608

774 Human 2.00E-05 47.64011 9060565423 9060565423 8989063403 8989063403 120613758 3 20613758

775 Human 0 78.77172 7616039154 7636039154 7559195039 7559195019 101185453 303 1 85453

776 Human 2.00E-05 47,69594 7426377836 7426377836 7369825033 7369825013 98726305 98726305

777 Human 0 79,64482 9302221036 9302221036 9229821859 9229821859 123719568 323719568

778 Humaii 4.00E-05 43,96215 9315643173 9315643173 9241283088 9241283088 124114349 124114349

779 Humaii 0 53,67736 8855979561 8855979561 8788164832 8788164832 117826681 117826681

780 Human ' 0 79,55218 8985286170 * 8985286170 89Ϊ652Ϊ677 8916521677 119482387 119482387

781 Human 0 79.51166 9796~136907 ' 9796136907 9725584948 9725584948 130301956 130301956

782 Human 0 61.74125 9163 180706 9161180706 9094159930 9094159930 123919617 121919617

783 Human 1.00E-05 50.42185 7404625600 7404625600 7348090449 7348090449 98600002 98600002

784 Human 3.00E-05 45.34464 6310495119 63104953 39 6259692997 6259692997 83945825 83945825

785 Human 0 78.69278 7403 894945 7401894945 7345429785 7345429785 98416034 98416034

786 Human 1.00E-05 50.30543 8943446846 8941446846 8873843270 8871843270 3 38958451 118958451

787 Human 6.00E-05 42.37466 8633979779 8633979779 8560733170 8560733370 3 34942141 114942343

788 Human 0 79.09541 8443230712 8443230712 8377452832 8377452832 112274944 112274944

789 Human 0 78.83376 ' 8049740331 8049740331^" ' 7988633705 7988633705 107122404 107122404

790 Human 0 79.28504 ' 8393509670 8393509670 ' 8330514064 8330514064 111597839 3 11597839

79 i Human 1.00E-05 49.3044 ' 7342642737 7342642737 ' 7285683657 7285683657 97645437 97645437

792 Human .00E-05 44.28692 9369604993 9369604991 9300446943 9300446943 124555199 324555199

793 Human 3.00E-05 44.69529 7087563660 7087563660 7032608777 7032608777 94253839 94253839

794 Human 0 78.93503 8226671492 8226671492 8161172358 8363 172158 109352883 309352881

795 Human 0 54.44015 256785541 3 2567855411 2490114384 2490114384 34249173 34249171

796 Human 0 60,98306 4297333742 4297333742 4255048638 4255048638 57107449 57107449

797 Human 3.00E-05 44,84428 1697187209 1697187209 1602691647 3602691647 22591337 22591317

798 Human 0 55,58743 4399955055 4399955055 4304217637 4304217637 58463335 58463335

799 Human ' 3.00E-05 45,22475 1162925120 ' ΪΪ62925120 1107249515 1107249515 15507716 15507716

800 Human 0 56.8148 Ϊ776565828 ^ Ϊ776565828 1732239431 1712239431 23655232 23655232

801 Human 9.00E-05 40.57542 Ϊ0675860086 ' Ϊ0675860086 10600742549 ' 10600742549 142050378 142050378

802 Human 0.00011 39.66393 9946570099 9946570099 9873478941 9871478941 132434756 132434756

803 Human 3.00E-05 44.91886 15634044994 1 5614044994 1553 5014965 15515034965 207991 166 207993 366

804 Human 6.00E-05 42.01341 7878322973 7878322973 7832938343 7812938343 304987419 104987419

805 Human 0 64.29747 11124438204 11124438204 10470156707 10470156707 353443751 151443751

806 Human 3.00E-05 45.81912 9342814462 9342814462 8784046099 8784046099 326956684 126956684

807 Human 6.00E-05 42.62116 8906528540 8906528540 8838919408 8838919408 118554849 118554849

808 Human 0 74.6979 11109062432 11109062432 10368074255 10368074255 152312596 152312596

809 Human 0 70.89489 ' Ϊ2462 Π06Ϊ6 Ϊ24621Ϊ06Ϊ6 * 12281858281 12281858281 167280519 167280519

810 Human 2.00E-05 47.40029 ' 9666949873 9666949873 ' 9603916507 9603916507 128470050 328470050

811 Human 5.00E-05 42.70132 9372623326 9372623326 9309776293 9309776291 124628368 324628368

812 Human 0 55.79195 10078016852 10078016852 10010500036 30030500036 134007399 334007199

813 Human 7.00E-05 41.64033 7763922383 7763922181 7707473893 7707473893 103285530 303285530

814 Human 0 70.32588 1 1263805983 1 3263805983 1 1077653988 3 3077651988 152360784 3 52360784

815 Human 4.00E-05 44.14361 10897031254 10897031254 10801546233 30801546233 145344492 345344492

816 Human l.OOE-05 51 ,53975 9598156877 95981 56877 9043466034 9043466014 132158347 332158347

817 Human 0 63,25522 8369583392 8369583392 8091465259 8091465259 113067658 113067658

818 Human Ϊ.66Ε-05 53,09128 12129844913 * Ϊ2Ϊ 298449 Ϊ 3 Ϊ 20 Ϊ 7642906 ' 12017642906 16Ϊ497302 161497302

819 Human 5.00E-05 43.081 39 13072523848 ' Ϊ3072523848 Ϊ296771190Ϊ ' 1296771 3901 175167321 175167321 Oxidation PF HQ PF HQ PF HQ PF HQ PF HQ PF HQ

Error Rate Oxidation Aligned Aligned Aligned Q20 Aligned Q20 Aligned Aligned

Organism OXO Q OXO Bases AP Bases Bases AP Bases Reads AP Reads

820 Human 0 79.38524 10763241705 10763241705 10674269002 10674269002 143378528 343378528

82 i Human 7.00E-05 4] , 68035 13074201947 13074201947 12969518088 12969518088 175214334 375214334

822 Flu man 0 80,32906 14455649477 14455649477 14356310582 14356310582 192847748 192847748

823 Flu man * Ϊ.00Ε-05 50,56182 8212477371 * 8212477371 8148640303 8148640303 109427699 109427699

824 Human 0 57.04263 12885255376 ' Ϊ2885255376 12790148371 ' 12790148371 173455984 171455984

825 Human 8.00E-05 41.16934 10295475194 ' Ϊ0295 75194 10205430710 ' 10205430710 137279341 137279341

826 Human 4.00E-05 44.58805 12278969560 12278969560 12381477784 12181477784 163646808 163646808

827 Human 0 56.79289 10280754074 10280754074 10397655371 10197655371 336893604 136893604

828 Human 3.00E-05 45.63234 12445073893 12445073893 12349436732 12349436732 366342492 166142492

829 Human 0 79.71006 11176431058 11176431058 11092716376 11092716376 148712660 148712660

830 Human i.OOE-05 49.8653 11059832234 11059832234 10973 358254 10971358254 147286858 147286858

83 i Human 0 79.33923 9350336242 9350336242 9280020269 9280020269 124480813 124480833

832 Human 1.00E-04 40.0189 11768463589 11768463589 11681957412 11681957412 157192718 157192718

833 Human 0 80.25047 * Ϊ3789398324 Ϊ 3789398324 ' Ϊ3683334435 13683334435 184186670 184186670

834 Human 0 79.6945 ' Ϊ1640400002 11640400002 ^ Ϊ1535832845 1 3535832845 155360164 355360164

835 Human 0 58.50733 13604025225 13604025225 13504901934 13504901914 181331570 381331570

836 Human 8.00E-05 43.20406 12041355397 12043355197 11943300692 3 3943300692 161281827 363 281827

837 Human 0 79.79958 9770317273 977033 7271 9689678803 9689678803 130090258 330090258

838 Human 0 80.22057 13096516084 13096516084 13000458230 33000458230 174469494 374469494

839 Human 0 79,56295 9143612094 914363 2094 9067714838 9067714818 121761436 323 761436

840 Human 4.00E-05 43,70513 10058168702 10058368702 9983711005 9983711005 134570104 334570104

841 Humaii 0 80, 16255 12755730675 12755730675 12662327875 12662327875 169949176 169949176

842 Humaii 0.00016 38,04709 10055805650 10055805650 9976879708 9976879708 133964295 133964295

843 Human ' 0.00013 38,74935 10750968784 ' Ϊ0750968784 10663798980 ' 10663798980 143260727 143260727

844 Human 0.00012 39.05854 6512481194 ' 651248 i 194 645671Ϊ898 6456711898 86845263 86845263

845 Human 0.00013 38.91173 10266351514 10266351534 10381297732 10181297732 136819729 136819729

846 Human 0.00016 38.10236 7654299169 7654299369 75903 36921 7590136923 303922222 101922222

847 Human 0.00013 38.78505 8939343579 8939343579 8866369889 8866369889 3 39214544 119234544

848 Human 0.00029 35.35032 9683065082 9681065082 9556759179 9556759379 330304568 130304568

849 Human 0.00011 39.5314 10893013886 10891013886 10805600862 10805600862 145234527 145234527

850 Human 0.00015 38.38334 7223525079 7223525079 7166939858 7166939858 96380057 96180057

851 Human 0.00013 38.78086 10734969403 10734969403 10656490997 10656490997 142851180 142851180

852 Human 6.00E-05 42.62508 ' Ϊ003396087Ϊ Ϊ003396087Ϊ ' 9955948336 9955948336 133894414 133894414

853 Human 8.00E-05 41.11441 ' Ϊ3396 74004 Ϊ3396474004 ' Ϊ3288969630 13288969610 179505442 379505442

854 Human 0.00052 32.8078 ' Ϊ1209495733 1120949570 ' 11129497538 1 3 329497518 149833694 349833694

855 Human 0.00086 30.64805 11301632301 11301632301 11218005302 1 3218005302 150638105 350638105

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857 Human 0.00334 28.73354 11935908090 1 3935908090 11847418873 3 3847418873 159414072 3 59414072

858 Human 2.00E-05 47,81035 9964252616 9964252616 9886564298 9886564298 132830733 332830733

859 Human 0 78,54557 12866751570 12866751570 12753491673 12753491673 171435230 373435210

860 Human 8.00E-05 40,8185 11949941360 11949941360 11858561606 1 3858561606 159363825 3 59363825

861 Human 6.00E-05 41,92426 4106070593 4106070593 3977684350 3977684350 54919470 54919470

862 Human ' 0 79, 15988 Ϊ524Ϊ5Ϊ4880 ' ^"15241514880 15139169591 ' 15139169591 203Ϊ9Ϊ076 203191076

863 Human 3.00E-05 45.4633 Ϊ 1564287749 ' Ϊ1564287749 i 1430565019 ' 11430565019 153658499 153658499

864 Human 6.00E-05 42.52035 10559763701 ' Ϊ055976370Ϊ Ϊ0435Ϊ73636 ' 10435173636 140403720 140403720

865 Human 4.00E-05 43.66698 12303971715 12303971735 12369190648 12169190648 163438509 163438509

866 Human 4.00E-05 43.5293 3 1 3650909646 11650909646 1 353 5779678 11515779678 354867700 154867700

867 Human 0 78.5628 8225903379 8225903379 8333472277 8131472277 309361933 109363933

PF Reads PF Unique PF Unique

PF Noise PF Noise PF Reads PF Reads Aligned PF Reads Bases Reads

Reads AP Reads PF Reads AP Al HS AP Aligned Aligned Aligned4 3873 3873 94373406 94373406 94373406 93575033 93575031 5920646847 785196615 4369 4369 108906276 108906276 108906276 106672185 106672185 6594831732 882635026 4490 4490 112180440 112180440 112180440 107725573 107725573 6399586661 864600027 4492 4492 110584100 110584100 110584100 109620647 109620647 6877493740 9Ϊ21082Ϊ8 4493 4493 111777798 ΪΪ1777798 3 11777798 1 30840338 110840338 6999222034 928028249 4147 4147 97631870 97631870 97631870 96855888 96855888 6108333428 810014510 4185 4185 101611244 101611244 301611244 100802704 100802704 6351625632 84231120! 5620 5620 137973526 1 37973526 337973526 335336214 135336214 6005580384 799889932 3711 371 1 86196086 86196086 86196086 85449795 85449795 4268339225 565588513 1616 1616 142358184 142358184 342358184 139020809 139020809 9159082368 3 215780114 1531 1 531 65701896 65701896 65701896 6453 3694 64533694 4344733244 574962615 1494 1494 139564818 1 39564818 339564818 136916961 136936961 8933937754 3 185581646 34009 34009 140617438 140617438 140617438 138918092 138918092 8315919351 1119865177 35941 35941 ' Ϊ453 Ϊ6570 145316570 145316570 143907332 ' Ϊ439Ό7332 8496223793 1144683798 35552 35552 144435408 144435408 144435408 142755905 142755905 8440352555 1134835259 32288 32288 135621512 135621512 135623512 1340591 35 134059115 7915377430 1065383240 30109 30109 124573084 124573084 124573084 122947333 122947133 7455151027 1003070741 362.91 36291 147594570 147594570 147594570 145866020 145866020 8644247139 11639657.02 34852 34852 143170020 14317002.0 143170020 141616858 141616858 8353144452 1123450673 32744 32744 132296090 132296090 132296090 130696140 130696140 7736418646 10403 39074 31450 31450 132304738 132304738 132304738 130878602 130878602 7800442621 1049033645 32285 32285 134250434 134250434 134250434 132722292 132722292 7932732033 1066817196 34013 34013 139144460 139144460 139144460 137635476 137635476 8186670409 1099660657 30774 30774 126656466 ^"126656466 126656466 125161793 125161793 7442747737 1001891848 33101 33101 135794634 335794634 335794634 133929043 133929043 7803893926 1051286039 3 127 34127 140096490 140096490 340096490 138343904 138343904 8151632872 1096153550 31724 3172.4 128997840 1 2.8997840 3 28997840 327540215 1275402.15 7688054463 103672273! 27852 27852 1 15427180 1 15427180 3 3 5427180 3 33996335 1 33996335 681633 5648 917903122 28933 28933 1 15207578 1 15207578 3 3 5207578 3 33794177 1 33794177 6892485173 92.6323363 31SS7 31887 130525506 1 30525506 330525506 129021603 129021603 7606390968 3023483014 34175 341 75 142813498 142813498 342813498 140717667 14073 7667 8257345570 3 110827955 30742 30742 124473652 124473652 124473652 122881528 122881528 7342845280 989991706 31233 31233 * Ϊ27368550 127368550 127368550 125939388 ' Ϊ25939388 7654966680 1029121117 29710 29710 122453328 122453328 122453328 120776478 120776478 7286439812 979777888 31380 31380 128980376 128980376 128980376 126961675 126961675 7453708369 1003801419 34621 34621 141799682 141799682 141799682 139678443 139678443 7962586571 10722038600 35169 35169 145743746 145743746 145743746 14401 3093 144011093 842.0712877 11337764601 32871 32871 134300092 134300092 134300092. 132827589 132827589 7874985228 10580967902 40204 40204 164247800 164247800 164247800 162128532 162128512 8776354800 11794988603 27708 27708 114887626 114887626 114887626 113632894 113632894 6933476186 9336098404 33751 33751 138766866 138766866 138766866 137141539 137141519 8020063370 10777360005 31374 31374 128453054 128453054 128453054 127064187 127064187 7760018346 10436953706 32114 32114 131963654 131963654 131963654 130576799 130576799 7858250648 10561281207 32754 32754 133383996 133383996 333383996 131697526 133697526 7747941865 10421075908 66938 66938 272767842 272767842 272767842 269672875 269672875 13492378590 18081701509 31342 31342 130254362 130254362 330254362 128401020 128401020 7646326932 10282086210 28705 28705 1 19493448 1 19493448 3 39493448 3 37984502 1 37984502 7007955196 943752541 1 32925 3292.5 135591490 1 35591490 335591490 333814514 133814514 7892501 857 10619902312 28444 28444 116335194 1 16335194 3 36335194 1 3 5002149 115002149 6924205208 9317982013 26S59 26859 109454312 109454312 309454312 108385965 108385965 6509800836 8744407314 32800 32800 131926542 131926542 131926542 130359497 130359497 7632924571 10267353615 33959 33959 139872874 139872874 139872874 138071208 138071208 8116928698 10915893516 34266 34266 ' Ϊ39438798 139438798 139438798 137855182 ' Ϊ37855Ϊ82 8078649362 10857239717 28727 28727 119652484 Ϊ Ϊ9652484 119652484 117910582 117910582 6945026145 9342385618 35936 35936 147347050 147347050 147347050 1455951 33 145595113 8380757317 11289965719 33435 33435 135645630 135645630 135645630 133945395 133945395 7898592253 1062248482.0 3272.3 32723 133764448 133764448 133764448 131862468 131862468 7702530610 1036202052.1 35980 35980 1478921 10 1478921 10 1478923 30 145858658 145858658 8377082978 1129631 5422 29977 29977 120914508 120914508 120914508 119429304 119429304 7096882993 9531883 223 31 579 31579 126768890 126768890 126768890 125240688 125240688 7424819252 9982995824 29443 29443 121232034 121232034 121232034 119755483 119755483 7208483356 9697997225 35252 35252 145109894 I 45109894 145109894 143129249 143129249 8343231628 ΙΪ2Ϊ9667926 31060 31060 125834454 125834454 325834454 124212093 124212093 7428600443 99937323 PF Reads PF Unique PF Unique

PF Noise PF Noise PF Reads PF Reads Aligned PF Reads Bases Reads

Reads AP Reads PF Reads AP Al HS AP Aligned Aligned Aligned rn 30690 30690 128117754 128137754 128117754 126641803 126641803 7457272767 100397226

328 32985 32985 137069178 137069378 137069378 134889227 134889227 8114810707 109434286

129 31243 31243 126084470 126084470 126084470 124532706 124532706 7321703630 98475362

130 29743 29743 122054180 ^"122654180 122054180 120777162 120777162 7357354773 98836680

131 24501 24501 99088576 99088576 99088576 14843597 14843597 496508818 7450256

132 31577 31577 130265792 Ϊ 30265792 330265792 128527234 128527234 7428070759 100134521

133 20249 20249 80135596 80135596 80135596 77184035 77384035 4221887376 57002323

134 26781 26781 106962066 306962066 306962066 302338760 102338760 6470633735 87334455

135 20619 20619 82487256 82487256 82487256 80324214 80324214 4242547431 56986443

136 22468 22468 90409832 90409832 90409832 87472645 87472645 5074602326 68414310

137 36556 36556 151584100 351584100 351584100 150009886 150009886 8722325553 3 17180095

138 41145 41 145 173232450 373212450 373212450 168717421 168737421 7844267280 305419360

139 30931 30931 124620040 124620040 124620040 123086970 123086970 7496432607 100747847

140 30759 30759 ' 125300166 125300166 125300166 123745557 *^" Ϊ23745557 7396064383 99473944

141 33301 33301 134350050 134350050 134350050 132477726 132477726 7850467701 105542613

142 35098 35098 143124246 143124246 143124246 139033458 139033458 2306668933 30803834

143 40855 40855 166832628 166832628 166832628 157195901 157195903 2703941539 36574322

144 39666 39666 162526476 162526476 162526476 158120737 158120737 7566965467 103939552

145 31879 31879 128701634 128701614 128703634 126918977 126918977 7767276433 104757071

146 33113 33113 137389552 137389552 137389552 135610095 135610095 8206323377 110433495

147 35889 35889 144815050 144835050 144815050 143050275 143050275 8509496602 114440782

148 29460 29460 119911410 119911410 119911410 116947850 116947850 2177177513 29070209

149 12147 12147 48568380 48568380 48568380 45731644 45731644 1695838678 23010321

150 9587 9587 144873842 I 44873842 144873842 143468119 143468119 7661726073 ^"101856597

151 6817 6817 96433666 96413666 96413666 95697748 95697748 5846829322 77735061

152 11326 3 1326 171626946 171626946 371626946 170624837 170624837 9309306937 123715007

153 9504 9504 143053696 141051696 341051696 339774115 139774115 7956873581 105773756

154 10172 30172 148368228 148168228 348168228 346940282 146940282 8233 394481 309420108

155 10053 30053 153862612 351862612 351862612 350558128 150558128 8483305706 1 12725622

156 29890 29890 358904224 358904224 358904224 355570021 355570021 15290329004 203640311

157 10208 302.08 151023144 351023144 351023144 149805601 149805601 8282823332 3 10082918

158 10824 10824 160219868 160219868 160219868 159046813 159046813 8739032789 116075421

159 6935 6935 * Ϊ62946428 Ϊ02946428 102946428 102303129 ' Ϊ02303Ϊ29 5635133238 74826948

160 9529 9529 143736188 143736388 143736388 142612237 142612237 7965378549 105867333

161 30727 10727 156697296 Ϊ56697296 156697296 155676473 155676473 8572008392 113925897

162 10503 10503 151813274 151833274 151813274 150767558 150767558 8452976636 112322202

163 10050 10050 150154068 150354068 150154068 149139764 149139764 8289550615 110337450

164 10439 10439 154449348 154449348 154449348 153246565 153246565 8548979814 113609487

165 9367 9367 144849098 144849098 144849098 143679208 143679208 8038050051 106950375

166 1 1 174 11174 162699710 162699710 162699730 161189758 161189758 8706328274 115766349

167 10446 10446 154285272 154285272 154285272 153067354 153067354 8467829757 112528369

168 8312 8312 121532336 121532336 121532336 120319586 120319586 6996450184 93066120

169 11714 11714 172414694 I 72414694 172414694 170906357 170906357 9229444262 Ϊ 225980 1

170 10274 30274 154235482 354235482 354235482 153049244 153049244 8470085209 112520030

171 4689 4689 84836368 84836368 84836368 84168818 84368818 4859936190 64599626

172 10454 30454 160274996 160274996 360274996 159038670 159038670 8663740747 115165742

173 7815 7835 133693726 1 13693726 3 33693726 3 32677948 132677948 6486240370 86294699

174 8829 8829 135247328 135247328 335247328 334340715 134340715 7583887209 100866878

175 10443 30443 151655452 351655452 351655452 150558789 150558789 8421559348 3 11934002

176 11797 3 3797 171022702 371022702 371022702 1693339 1 169333931 8937656031 3 18705488

177 10171 10171 150276480 150276480 150276480 148753063 148753063 8412400329 112106902

178 8846 8846 132991350 132991350 132991350 131822964 131822964 7694062029 102397707

179 9537 9537 ' Ϊ3975Ϊ666 Ϊ3975Ϊ666 139751666 138610966 ' Ϊ386Ϊ0966 7793¾8642 103621791

180 30574 10574 157017378 157037378 157017378 155670871 155670873 8631559817 114758139

181 3 1522 11522 165153196 165153196 165153396 163717446 163717446 8917486655 118460656

182 9531 9531 138969880 138969880 138969880 137867466 137867466 7919078599 105242327

183 22894 22894 282839392 282839392 282839392 279973395 279971395 13287883629 177433890

184 9650 9650 143048836 143048816 143048816 142017599 142017599 7974248717 106057918

185 9843 9843 147904956 147904956 147904956 146909735 146909715 8109604910 107730361

186 9643 9643 146003546 146003546 146003546 144908147 144908147 8006936047 106438883

187 10748 10748 163889480 163889480 163889480 162616315 16261631 9076470909 120640450

188 9080 9080 134545126 ^"134545126 134545126 133515887 133515887 7491437207 99634722

189 8658 8658 130358298 330158298 330158298 328960060 128960060 6948423956 92361893

PF Reads PF Unique PF Unique

PF Noise PF Noise PF Reads PF Reads Aligned PF Reads Bases Reads

Reads AP Reads PF Reads AP Al HS AP Aligned Aligned ASigned

253 5263 5263 49360068 49360068 49360068 48825435 48825435 3252038755 4316083 3

254 7781 7781 72982778 72982778 72982778 63617624 63617624 3 726498098 23729250

255 5835 5835 130338498 130338498 130338498 126034891 126034891 6771901241 91305348

256 6713 6713 149414112 149414112 149414112 141863638 141863638 7004761288 94381873

257 5050 5050 46451198 4645 ί 198 46451198 45941773 45941773 3002604608 39817694

258 5072 5072 133580032 Ϊ 33580032 333580032 131751913 133751913 7735365778 103311395

259 4909 4909 45985488 45985488 45985488 45651714 45651714 3079453260 40829910

260 6228 6228 145637126 345637126 345637126 343763456 143763456 7255364508 96748540

26 S 6320 6320 1983 38248 398118248 398118248 395537734 195537734 10465697630 3 39103846

262 1257 3257 40873040 40873040 40873040 40354733 40354733 2703680269 35837263

263 1286 3286 41634884 41634884 43634884 43239420 41239420 2742896315 36350212

264 1249 3249 42059756 42059756 42059756 43697025 41697025 2768764453 36691037

265 1333 1333 40927852 40927852 40927852 40542770 40542770 2690176018 35648454

266 1267 1267 ' 40503074 40503074 40503074 40210334 ' 40210334 2674485147 35433334

267 3309 1309 43108808 43108808 43108808 42798164 42798164 2843270510 37672386

268 3 184 1184 40100156 40100156 40100356 39621490 39621490 2641722383 35022034

269 495 495 208110254 2083 30254 2081 30254 206619050 206619050 3 1969664622 158620381

270 9622 9622 97033508 97033508 97033508 95956329 95956329 6148994208 81783006

27 i 8902 8902 86141946 86343946 86143946 85514725 85514725 5522226883 73228659

272 9335 9335 93236510 93236530 93236530 92373059 92373059 5866531723 77815080

273 6860 6860 69126020 69126020 69126020 68469770 68469770 4476606027 59423 559

274 9179 9179 87848702 87848702 87848702 87062481 87062481 5567708826 73877859

275 7801 7801 76886182 76886182 76886182 76119363 76119363 4922314640 65363448

276 8571 8571 86392578 86392578 86392578 85623537 85623537 5507665858 73091699

277 654 654 219279724 279279724 219279724 238013268 218013268 12619364771 167106734

278 566 566 226479866 226479866 226479866 224807989 224807989 12849891762 170249649

279 8227 8227 83703012 81701012 83 701012 83022215 83022215 5259259063 69810484

280 7929 7929 767773 16 76777116 76777116 76394804 76394804 4968858643 65909695

28 S 411 43 3 176594596 3 76594596 376594596 374945205 174945205 9960896615 3 32121783

282 7899 7899 82808702 82808702 82808702 73746202 71746202 1433046162 39833892

283 8945 8945 92437372 92417372 92417372 83547740 83547740 1672923 524 22962301

284 1021 Ϊ 10211 99306026 99306026 99306026 98500106 98500106 6179358811 81919783

285 Ϊ05Ϊ5 10515 ' 17)5663726 105663726 105663726 104723700 ' Ϊ04723700 6524667825 86581442

286 8084 808 83657852 83657852 83657852 74683633 74683631 3214007410 44829303

287 9389 9389 93000846 93000846 93000846 88883543 88883541 3099353603 1866062

288 8697 8697 205254046 205254046 205254046 196200065 196200065 3501224446 47385136

289 8918 8918 90926688 90926688 90926688 84461679 84461679 3621189584 22373 534

290 9786 9786 95428938 95428938 95428938 89706893 89706893 3813968983 51635773

29 i 7845 7845 209136134 2091363 34 209136334 199389473 199389473 3380066189 45830430

292 8054 8054 197056524 197056524 197056524 185408226 185408226 3094430716 42397966

293 9976 9976 100538258 100538258 100538258 95229415 95229415 3866013018 52178795

294 1 214 10214 101623118 101623118 101623118 99324016 99324016 5359667193 71452344

295 9198 9198 89155874 89155874 89155874 85558097 85558097 1784699778 23984167

296 1616 3616 142358184 Ϊ 42358Ϊ84 342358184 139020809 139020809 9159082368 121578011

297 1531 3531 65701896 6570 ί 96 65701896 64513694 64533694 4344733244 57496261

298 1494 3494 139564818 139564818 339564818 136916961 136916961 8933937754 118558164

299 12996 3 2996 103387458 303387458 303387458 302362751 102362751 6528454314 86657825

300 13954 33954 106939588 306939588 306939588 305665742 105665742 6733433069 89351793

30! 14840 34840 118705450 3 18705450 3 3 8705450 1 37605670 117605670 7780758405 303215691

302 14465 34465 111549698 3 11549698 3 3 1549698 1 30248941 110248941 6993909512 92816715

303 16076 16076 124534238 124534238 124534238 123025480 123025480 8124302374 107823037

304 14373 14373 109084636 109084636 109084636 107559840 107559840 7120742429 94578068

305 Ϊ5567 15567 * 112349732 112349732 112349732 110886468 ' Π088646Ϊ 7038470391 93439883

306 33218 13218 100728032 Ϊ00728032 100728032 99577620 99577620 6388077062 84793600

307 33580 13580 104270032 104270032 104270032 103096734 103096734 6551744572 86943773

308 34543 14543 110281258 110283258 110283258 109140605 109140605 6920451303 91820867

309 34634 14634 115343636 115343616 115343636 114126274 114126274 7568275263 1003943 84

310 3 5688 15688 120224622 120224622 120224622 119053894 119051894 7562671979 100297049

311 34417 14417 104022388 104022388 104022388 102898993 102898993 6804076907 90294331

312 34203 14203 106282126 1062823 26 106282326 104928234 104928234 6827144337 90658885

313 14672 14672 110788374 110788374 110788374 109267771 109267771 6912350285 91766573

314 12610 12610 99658708 99658708 99658708 98744206 98744206 6315834837 83783887

315 13386 33386 101974226 301974226 301974226 100870173 100870173 6393337871 84825325 PF Reads PF Unique PF Unique

PF Noise PF Noise PF Reads PF Reads Aligned PF Reads Bases Reads

Reads AP Reads PF Reads AP Al HS AP Aligned Aligned Aligned

316 15435 15435 126804086 126804086 126804086 125477665 125477665 7865043553 104370468

317 14676 14676 113208546 113208546 113208546 111925439 111925439 7371781179 97837071

318 14726 14726 110356432 110356432 110356432 109196734 109196734 6977269901 92570083

319 14468 14468 107468622 ^"107468622 107468622 105979518 105979518 6978060503 92682083

320 15453 35453 121978858 121978858 321978858 120405808 120405808 7894045021 104810055

321 15806 35806 117280540 Ϊ Ϊ7280540 3 17280540 105152900 105352900 5759634902 76342299

322 13591 33591 103278154 103278154 303278154 101610541 103610541 6541876543 86838820

323 13758 33758 130644274 3 10644274 3 30644274 309510521 109530521 6917028369 91789650

324 13901 33901 107034858 307034858 307034858 305827825 105827825 6673447808 88532498

325 15955 35955 123352764 323152764 323152764 123783012 123783012 8037864251 306664558

326 12936 32936 95879942 95879942 95879942 94870791 94870791 6023063835 79933922

327 15062 35062 109734178 309734178 309734178 108429591 108429591 7099470935 94265668

328 15356 15356 111929170 111929170 111929170 110312461 110312461 7162812171 95078447

329 Ϊ4729 14729 ' Ϊ09099006 Γ09099θ^"θ6 109099006 107754915 ' Ϊ07754915 68Ϊ0Ϊ40Ϊ52 90390875

330 33292 13292 102095434 Ϊ02095434 102095434 100926377 100926377 6474858502 85922427

33 i 34398 14398 106058188 106058188 106058388 104576032 104576032 6627399629 87973459

332 34053 14053 105458736 105458716 105458736 104209602 104209602 6677131330 88606202

333 36001 16003 127811742 12783 3742 12783 3742 124232058 124232058 8083451523 107394424

334 34621 14623 109408956 109408956 109408956 108198409 108198409 6885527005 91309243

335 34803 14803 110968112 1109683 12 1109683 32 109601883 109601883 7179147528 95289468

336 34614 14614 115275194 115275394 115275394 113943454 113943454 7418653968 98472302

337 14973 14973 112069216 112069216 112069216 110584584 110584584 6971146871 92564472

338 14030 14030 103174208 103174208 103174208 102041598 102041598 6503705790 86295318

339 14533 14533 106258240 ^"106258240 106258240 105110702 105110702 6659830782 88379602

340 14504 34504 115323164 115123164 3 15123164 133861209 113861209 7194357045 95485918

341 17400 37400 133793960 133793960 333793960 129892299 129892299 7145409833 95321512

342 14397 34397 103565450 303565450 303565450 302220412 102220412 6428969054 85367867

343 15809 35809 122338162 322138162 322138162 320448428 120448428 7650379303 301644644

344 15125 35325 134333326 3 14131326 3 34131326 3 32823853 132823853 7475038457 99185810

345 14873 34873 111989306 3 11989306 3 3 1989306 130464403 110464403 6965242206 92471666

346 12993 32993 98946086 98946086 98946086 97834102 97834102 6248384424 82942258

347 16173 16173 124621984 124621984 124621984 122849797 122849797 7565434176 100423273

348 14941 14941 ' 110488242 110488242 110488242 109312751 ' ^"109312751 6932263413 91979742

349 35556 15556 117450828 l^" 17450828 117450828 114815138 114815118 7591138407 100691515

350 34766 14766 107505496 Ϊ07505496 107505496 106464637 106464637 6637276214 88047060

351 35268 15268 120832608 120832608 120832608 118978302 118978302 7730884433 102654286

352 34412 14412 114922468 114922468 114922468 113449930 113449930 7315132147 97308089

353 34212 14212 108830930 108830910 108830930 107378675 107378675 6831356419 90682228

354 34527 14527 104705064 104705064 104705064 103530999 103530999 6623923499 87897374

355 35085 15085 116125124 116125324 116125324 114576237 114576217 7107301728 94326520

356 33002 13002 104793934 104793934 104793934 103287127 103287127 6591745320 87505377

357 15228 15228 117039898 117039898 117039898 115708639 115708639 7672051846 101804584

358 15564 15564 120105358 ^"120105358 120105358 118461538 118461538 7379884370 97954215

359 13952 33952 106912678 106912678 306912678 105411720 105411720 6822734075 90615980

360 15166 35166 117972358 Ϊ Ϊ7972358 3 17972358 136483140 116483140 7709592889 102325161

361 14235 34235 108695250 108695250 308695250 107454653 107454653 6912534960 91720572

362 12956 32956 95023512 95021512 95021512 93889580 93889580 6025474330 79986242

363 14433 34433 107773106 307773106 307773106 306477661 106477661 6727732063 89243192

364 13810 33810 106538194 306518194 306518194 105391398 105391398 6664867132 88453108

365 14992 34992 111432654 3 11432654 3 3 1432654 130300317 110300317 7313072011 97072582

366 15194 15194 119048278 119048278 119048278 117632041 117632041 7311465238 97029763

367 14625 14625 108313940 108313940 108313940 106827895 106827895 6984818918 92743944

368 7Ϊ42 7142 ' 88354252 88354252^" 88354252 87Ϊ3655Ϊ ' 87136551 52845562Ϊ8 70256898

369 6879 6879 85008754 85008754^" 85008754 83997272 83997272 5243650666 69663030

370 5489 5489 66849682 66849682 66849682 66342796 66342796 4347023169 57676358

37 i 5479 5479 70191500 70393500 70193500 69525238 69525218 4513935885 59933841

372 6253 6253 80925578 80925578 80925578 79980707 79980707 5081002880 67505767

373 4794 4794 59396176 59396376 59396376 58819620 58819620 3865480250 51309496

374 5295 5295 68128950 68128950 68128950 67486134 67486134 4340648138 57634331

375 7340 7340 92107624 92107624 92107624 90972224 90972224 5446283222 72344436

376 5821 5821 70802276 70802276 70802276 70075389 70075389 4501294084 59779198

377 5954 5954 74862326 74862326 74862326 74197018 74197018 4705495751 62467382

378 5001 5001 63187130 63187Ϊ3 63187130 62570683 62570683 4065282400 53979008 PF Reads PF Unique PF Unique

PF Noise PF Noise PF Reads PF Reads Aligned PF Reads Bases Reads

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379 5969 5969 76377502 76377502 76377502. 75707810 75707810 4823690685 64033991

380 4953 4953 63132348 63132348 63132348 62533517 62533517 4064534666 53964054

381 5371 5371 70866810 70866810 70866810 70137304 70137304 4441201543 58999559

382 4794 4794 55577856 55577856 55577856 52709344 52709344 41867220 575483

383 5193 5193 64303320 64303320 64303320 63763643 63763643 4134832146 54884216

384 5994 5994 74503924 74503924 74503924 73783829 73783829 4746999929 63020419

385 6314 6314 78291212 78291212 78291212 77506576 77506576 4958309625 65869341

386 6090 6090 78104888 78104888 78104888 772.34831 77234831 4935652.682 65553894

387 5826 582.6 73090456 73090456 73090456 72404682 72404682 4668766098 61987487

3S8 5895 5895 73461816 73461816 73461816 72636953 72636953 4692334056 62298027

389 5168 5168 62498282 62498282 62498282 59190638 59190638 56422757 779802

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392 5820 5820 ' 72558532 72558532 72558532 71906320 ' 71906320 4630600256 61492835

393 5751 5751 69585700 69585700 69585700 68889717 68889717 4410965327 58572042

394 5655 5655 70883478 70883478 70883478 70132600 70132600 4434976857 58878193

395 4981 4981 62019690 62019690 62019690 61388451 61388451 3960770702 52620087

396 6266 6266 78849150 78849150 78849150 78079609 78079609 4973130413 66039005

397 5917 5917 731 12522 731 1252.2. 73112522. 72277733 72277733 4645663165 61680565

398 5614 5614 68789326 68789326 68789326 68086619 68086619 4444179985 59028345

399 6067 6067 75229810 75229810 75229810 74068407 74068407 4701765645 62584962

400 6793 6793 85853192 85853192 85853192 84592622 84592622 5262913248 69983036

401 6865 6865 84678462 84678462 84678462 83576126 83576126 5172578486 68744133

402 6299 6299 78356412 78356412 78356412 77499748 77499748 4889981778 64938950

403 5831 5831 73939992 73919992 73919992 73164364 73364364 4714223561 62571034

404 5325 5325 65323812 65323812 65323812 64743446 64743446 4212734952 5590404

405 5843 5843 74840082 74840082 74840082 74089895 74089895 4719027863 62.666989

406 5444 5444 70047000 70047000 70047000 69387870 69387870 4467643555 5931 1601

407 7613 761 3 91223572 91223572 91 2.2.3572 90148895 90348895 5298332.049 70349420

408 5143 5143 65313504 65313504 65313504 64771768 64773 768 4198343237 55718702

409 6162 6162 73635976 73635976 73635976 72986885 72986885 4670899077 62018884

410 5068 5068 61008190 61008190 61008190 60434243 60434243 3865322393 51308930

411 5255 5255 ' 67 19024 67819024 67819024 67180736 ' 67180736 4342709632 57659627

412 4727 4727 58335602 58335602 58335602 57681884 57681884 3733253871 49596483

413 4814 4814 61092472 61092472 61092472 60558372 60558372 3971727828 52693419

414 5705 5705 71654034 71654034 71654034 70831174 70831174 4531876173 60199702

415 4820 4820 60728198 60728198 60728198 60142009 60142009 392.2170470 52073491

416 7502. 7502 91814058 91814058 91814058 90496454 90496454 552.5275006 73462685

417 5638 5638 71408466 71408466 71408466 70726155 70726155 4485290238 59564885

418 5696 5696 73405534 73405534 73405534 72717009 72717009 4656670706 61816349

419 51 82 5182 65379676 65379676 65379676 64862476 64862476 4202995633 55778930

420 5533 5533 69730488 69730488 69730488 68897754 68897754 4447213584 5906 145

421 6021 6021 73688900 73688900 73688900 72980643 72980643 4700270470 62396072

422 4983 4983 60395722 60395722 60395722 59854093 59854093 3907695517 51867846

423 6336 6336 75952758 75952758 75952758 74811079 7483 1079 4703308629 62559854

424 5784 5784 73809372 73809372 73809372 73019586 73039586 4671478920 62023309

425 6043 6043 75309532 75309532 75309532 74595381 74595381 4708028185 62.530356

426 7390 7390 9181 5164 91815164 91 815164 90406493 90406493 54107352.16 71967495

427 5625 5625 70630882 70630882 70630882 69836327 69836327 4449420584 59100913

428 5510 5510 68836676 68836676 68836676 68052371 68052371 4350428009 57790961

429 5480 5480 70650702 70650702 70650702 69870551 69870551 ό ¾ ¾ 3 A-A- 3 59735995

430 5609 5609 69207712 69207712 69207712 68548164 68548164 4448848563 59061383

431 4339 4339 ' 52711012 52711012 52711012 522Ϊ0217 ' 52210217 3433116761 45566850

432 5653 5653 70512882 70512882 70512882 69746989 69746989 4444309477 59002574

433 5484 5484 69098804 69098804 69098804 68358699 68358699 4382824275 58206321

434 5770 5770 67261724 6726172.4 67261724 66590122 66590122 4313938650 5725591 8

435 652.0 6520 78729464 78729464 78729464 77989555 77989555 4944020484 65634074

436 5696 5696 73017018 7301701 8 7301701 8 72122302 72122302 4593071703 61005571

437 5537 5537 68541006 68541006 68541006 67901308 67901308 4383139169 58188541

438 5355 5355 66129176 66129176 66129176 65462251 65462251 4265751649 56630867

439 5585 5585 68212454 68212454 68212454 67609575 67609575 4392050014 58293822

440 5293 5293 66320470 66320470 66320470 65584355 65584355 4225430928 56101817

441 5074 5074 61565428 61565428 61565428 60931177 60931177 3918873037 52023967

PF Reads PF Unique PF Unique

PF Noise PF Noise PF Reads PF Reads Aligned PF Reads Bases Reads

Reads AP Reads PF Reads AP Al HS AP Aligned Aligned Aligned

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506 255 255 89597932 89597932 89597932 88862600 88862600 5553833625 73974263

507 233 233 93918514 93918514 93918514 93160101 9 160101 5898535350 78476273

508 300 300 103063046 103063046 103063046 101695244 101695244 6282231340 83903355

509 250 250 83349472 83349472 83349472 82389008 82389008 5214635155 69480876

510 275 275 104446486 304446486 304446486 103372155 103372155 6401555960 85281203

511 265 265 95706622 95706622 95706622 94587638 94587638 5946803885 79286630

512 234 234 93178512 93178512 93178512 92162426 92362426 5794465987 77185132

513 275 275 92652536 92652536 92652536 93 834206 91834206 5742462717 76454619

514 234 234 93410946 93410946 93410946 92534706 92534706 5848837855 77883280

515 266 266 97123564 97123564 97123564 96242954 96242954 6077448534 80911999

516 246 246 91472546 91472546 93472546 90704913 90704913 5770595628 768 1481

517 223 223 93992684 93992684 93992684 92901469 92901469 5770789036 76952392

518 25Ϊ 251 ' 96467534 96467534 96467534 95546506 ' 95546506 5890250482 78447637

519 264 264 106210208 106230208 106210208 104529603 104529603 6304825816 84256517

520 282 282 103886232 103886232 103886232 102815746 102815746 6302021730 83930316

521 278 278 104401130 104401 1 0 104403 330 103263538 103263538 6382854207 85075750

522 263 263 96799144 96799144 96799344 95655425 95655425 5932802007 79045305

523 262 262 91162622 91 162622 91162622 90387418 90387418 5706433028 75977973

524 309 309 111430900 111430900 111430900 109726652 109726652 6647296331 88745693

525 281 281 95261516 95263 5) 6 95261536 93856500 93856500 5550532740 73953472

526 271 271 94677948 94677948 94677948 93749942 93749942 5922313134 78866715

527 368 368 117499162 117499162 117499162 113963810 113963810 5351032971 71672384

528 293 293 114541080 Ϊ 14541080 114541080 113201412 113201412 6829688793 91090384

529 30 304 108212172 308212172 308212172 107089995 107089995 6456743214 85937724

530 333 333 128449076 128449076 328449076 125799809 125799809 7351499631 98419196

531 183 1 83 80492526 80492526 80492526 79726961 79726961 5026725797 67033051

532 341 341 1 18240524 1 18240524 3 3 8240524 1 36909251 1 16909251 6957902154 92688806

533 386 386 136050760 1 6050760 336050760 120996062 120996062 4483834962 61565375

534 289 289 104623330 304623330 304623330 103510100 103530100 6340938119 84481535

535 238 238 87909098 87909098 87909098 86935313 86935313 5420705954 72195312

536 283 283 92298068 92298068 92298068 91290138 91290138 5709761284 76022331

537 28Ϊ 281 ' Ϊ05460614 105460614 105460614 104105492 ' Ϊ04 ί 05492 5030598674 67008743

538 263 263 90232602 90232602 90232602 89147212 89147212 5527737204 73706975

539 257 257 221791238 221793238 221793238 220189636 220189616 11567258616 152989994

540 391 191 235201526 235201526 235203526 233287809 233287809 12717207028 168234347

541 70 70 161579360 161579360 161579360 160435103 160435103 8494081424 112533004

542 41 41 94725734 94725734 94725734 94042010 94042010 5843822105 77374789

543 84 84 156936684 156936684 156936684 155248448 155248448 4073624420 53964335

544 8342 8342 131190724 131190724 131190724 129977864 129977864 7767730597 103147031

545 9489 9489 148697828 148697828 148697828 146995743 146995743 8553909280 113635078

546 8849 8849 140471120 140471120 140471120 139195424 139195424 8310376249 110350384

547 8397 8397 130935192 ^"136935192 130935192 129797673 129797673 7638401109 101401913

548 8124 8124 128003478 I 28003 78 328003478 126731949 126731949 7555644050 100340780

5 9 832 8324 133474102 133474102 333474102 132218762 132218762 7846091881 104183869

550 7426 7426 110979034 3 10979034 3 3097903 109849023 109849023 6711279892 89186177

551 7158 7158 98145974 98145974 98145974 97105408 97305408 6001434781 79761175

552 8107 8107 126428430 1 26428430 3 26428430 125361619 125361619 7515395624 99823919

553 7253 7253 107874260 307874260 307874260 106852281 106852281 6575532869 87380948

554 9556 9556 152213448 3 52213448 3 52213448 147989762 147989762 8320323 377 3 11368356

555 7258 7258 114363118 114363118 114363118 105219703 105219703 6037483394 83786904

556 8835 8835 140065660 140065660 140065660 138652394 138652394 8221207090 109161346

557 6668 6668 ' Ϊ35667Ϊ24 Ϊ 35667124 135667124 129 17704 ' ^"129 17704 7558792799 102786625

558 8323 8323 132656928 Ϊ32656928 132656928 129335086 129335086 7397543689 99234819

559 7552 7552 113308062 113308062 113308062 112229441 112229443 6765195618 89856537

560 81 17 8117 129822894 129822894 129822894 128301658 128301658 7511777830 99834409

561 6804 6804 94868248 94868248 94868248 93924573 93924573 5742557068 76316779

562 8303 8303 126124418 126124418 12612441 8 124891990 124891990 7387327474 98198725

563 7826 7826 121603848 121603848 121603848 120299269 120299269 7134008942 94758234

564 7953 7953 123564678 123564678 123564678 122226240 122226240 7054494530 93759636

565 59608 59608 181487302 181487302 181487302 179651408 179651408 2938456495 39003734

566 68822 68822 208655640 208655640 208655640 204492113 204492113 2245289725 29972876

567 68387 68387 213369252 2Ϊ3169252 213169252 230206652 210206652 10073439041 334811832 PF Reads PF Unique PF Unique

PF Noise PF Noise PF Reads PF Reads Aligned PF Reads Bases Reads

Reads AP Reads PF Reads AP Al HS AP Aligned Aligned Aligned

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569 64734 64734 195356140 195356340 195356340 193942030 193942010 30656063873 141963584

570 68006 68006 206438126 206438126 206438126 199072222 199072222 1817799072 24462434

571 49289 49289 151186656 151186656 151186656 150151162 150151162 9132447580 121608233

572 51202 51202 158075576 3 58075576 358075576 156908362 156908362 9422342850 125620215

573 62559 62559 192939416 192939 16 392939416 185201427 185201427 816134364 11012085

574 66144 66144 199360464 199160464 399160464 197809346 197809346 10106833858 134300186

575 73427 73427 223902402 221902402 221902402 239690634 239690634 3618380232 48017043

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580 78727 78727 238726610 238726610 238726610 235364534 235364534 13173606350 176138700

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583 649610 649610 136650132 136650132 136650332 133835885 133835885 8319948813 110998087

584 550952 550952 115644226 115644226 115644226 108863796 108863796 6731559713 89850260

585 845992 845992 171668570 173668570 171668570 167503044 167501044 9327291543 124436014

586 71 5522 715522 141181046 143 383046 141183046 137220334 137220134 8522201636 113935685

587 570728 570728 121703202 121703202 121703202 118390262 118390262 7269129551 97166837

588 690919 690919 142369364 142369364 142369364 139498449 139498449 8196515849 109433465

589 620995 620995 131669638 131669638 131669638 129098314 129098314 8196827580 109598768

590 547873 547873 117368738 117368738 117368738 110946978 110946978 6777405672 90456277

591 813394 813394 171080868 171080868 171080868 167540370 167540370 6638695450 88235439

592 716583 716581 145366072 145366!) 72 345366072 141925013 143925013 7510855406 100418806

593 1046852 3046852 2033 11800 203111800 203111800 195777467 195777467 8635351461 115530612

594 877762 877762 173440002 3 73440002 373440002 369548730 169548730 10232034897 3 36202402

595 1077700 3077700 232777750 212777750 23 2777750 202504350 202504350 7448623370 300446384

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598 678952 678952 143420784 343420784 343420784 1403 24736 140324736 8301240935 3 10781368

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603 958350 958350 193269438 193269438 193269438 183164527 183164527 9318483685 125601774

604 730330 730330 155848240 155848240 155848240 150990080 150990080 8373498869 112055316

605 683558 683558 142577496 142577496 142577496 138433445 138433445 7952894040 1064763 39

606 733873 733873 157442728 157442728 157442728 153382745 153382745 8172413501 109294242

607 8) 8568 818568 163875324 163875324 163875324 159429452 159429452 8914658168 119287650

608 6) 9844 619844 130940734 130940734 130940734 127583744 127583744 7679360398 102785921

609 889317 889317 176139854 176139854 176139854 171789666 171789666 9961438292 132845943

610 664291 664291 142744408 142744408 142744408 138542626 138542626 8085775367 108291669

611 842003 842003 175094142 175094142 375094142 170520356 170520356 9733433363 130163113

612 733306 733306 156923906 156923906 356923906 153447176 153447176 8915308148 118980632

613 925210 925210 188567474 188567 74 388567474 183844525 183844525 9608501596 128358527

614 1002279 3002279 192830900 392830900 392830900 383930124 183930124 8683863 809 3 17051267

615 911910 93 3910 179007362 3 79007362 379007362 372456832 172456832 9572562381 3 28541223

616 689486 689486 147243892 347243892 347243892 143457579 143457579 8062455330 307648780

617 603326 603326 129569266 3 29569266 329569266 123972993 123972993 6991025114 93960961

618 730742 730742 151015690 151015690 151015690 138254834 138254834 6484402689 88040842

619 891904 891904 178566298 178566298 178566298 173240292 173240292 9374607581 125421783

620 759955 759955 ' Ϊ47960734 Ϊ47960734 147960734 143904353 ' Ϊ43904353 8048872509 107684144

621 794831 794831 158102478 158102478 158102478 154979524 154979524 9339531254 124478485

622 699010 699010 141321294 141321294 141323294 138506434 138506414 8364841056 111556857

623 755682 755682 150082462 150082462 150082462 146927740 146927740 8867026584 1184373 19

624 692210 692230 143691020 143693020 143693020 140967685 140967685 8473681094 113322637

625 583160 58 160 125158666 125358666 125158666 122623 386 122621186 7553380136 100909062

626 703962 703962 142659878 142659878 142659878 139504798 139504798 8493444126 113428435

627 524111 524111 113608832 113608832 113608832 111203877 111203877 6983257765 93283066

628 790735 790735 156482018 156482018 156482018 153144348 153144348 9143309403 122014370

629 644607 644607 133250536 133250536 133250536 130624024 130624024 7832831417 Ϊ04688490

630 717865 717865 143358564 Ϊ 4315 564 343158564 140151611 140351611 8569230842 114409013 PF Reads PF Unique PF Unique

PF Noise PF Noise PF Reads PF Reads Aligned PF Reads Bases Reads

Reads AP Reads PF Reads AP Al HS AP Aligned Aligned Aligned i 821327 821327 163214172 1632343 72 163234372 159618633 159618633 9544686747 1272962322 799724 799724 157483844 157483844 157483844 153830666 153830666 9372802685 1249977683 798429 798429 157090614 157090614 157090614 153569612 153569612 9175993863 1224193554 562708 562708 121247446 121247446 121247446 118806463 118806463 7426449738 990 12805 456818 456818 99456786 99456786 99456786 97411300 9743 1300 6124927157 818038406 670658 670658 142409580 Ϊ 42409580 342409580 139618114 139618114 8099339479 1079528147 731734 731734 149597800 149597800 349597800 146887809 146887809 8877635478 1184454178 588228 5882.28 1 37372756 3 17372756 3 3 7372756 3 34574580 1 34574580 6773394548 909568079 869675 869675 175394686 3 75394686 375394686 37382.9100 173829100 8850034985 3 179477530 732866 732866 157349474 3 57349474 3 57349474 354298682 154298682 8383626691 3 11660625 i 1125600 3 325600 237400312 217400312 23 7400312 23 3798458 23 3798458 5840367883 779071832 694619 694619 236328718 216328718 236328718 23 3600967 23 3600967 2020728569 269267733 719187 719187 150745626 150745626 150745626 147455249 147455249 8541827834 1141289854 976Ϊ99 76199 ' Ϊ9836Ϊ864 198361864 198361864 189285669 * Ϊ 92 5669 8412419630 1132028635 3045595 1045595 206659754 206659754 206659754 198299860 198299860 9635794283 1293369556 673577 673577 142098554 142098554 142098554 136776041 136776043 7392293523 990933087 673159 673159 142473994 142473994 142473994 138778854 138778854 802.4528838 1072275768 1711048 1711048 354367366 354367366 354367366 342188393 342188193 3 3730097048 18373 39699 662266 662266 140355970 140355970 140355970 134099309 134099309 6772220347 910225210 710804 710804 144574186 1445743 86 144574386 141576808 141576808 8442824923 112606511 i 692505 692505 143901634 143903634 143903634 141053499 141053499 8537900204 1140550082 974092 974092 194164544 194164544 194164544 189103669 189103669 8874686063 1184911363 684854 684854 138990920 138990920 138990920 135907730 135907730 8070759993 1076349854 754607 754607 150772854 ^"150772854 150772854 147760193 147760193 8892657440 ΙΪ85783215 45 45 103082594 Ϊ 03082594 303082594 97570694 97570694 4609999068 611672666 32 32 116506142 116506142 3 16506142 1 30849435 110849435 5004380531 663644097 32 32 108976730 308976730 308976730 302934091 102934091 4519543065 599757238 47 47 132254848 3 32254848 332254848 325260387 125260387 5363280987 711229999 35 35 122743980 3 2.2743980 3 22.743980 3 36460333 1 36460333 4989478115 662688430 32 32 94723012 94721012 94721012 89609809 89609809 4086398947 54234487! 51 53 143222646 343222646 343222646 335905740 135905740 5305264686 704057442 36 36 107405220 107405220 107405220 101980411 101980411 4592684687 609357073 33 33 ' 6800604 96800604 96800604 91028719 ' 910287Ϊ9 4Ϊ9Ϊ 89270 556267384 31 31 115752032 115752032 115752032 109271930 109271930 5109449269 679925785 38 3 117436982 117436982 117436982 1110351 33 111035113 4739102214 629903736 26 26 106861410 106861410 106863410 10194523 1 10194521 3 4576593161 607237707 29 29 101558480 103558480 101558480 96708069 96708069 4204730686 557866598 22 ^,-> 97169228 97369228 97169228 91755995 91755995 3999464533 533446449 69 69 279907278 279907278 279907278 268255903 268255903 7227305563 9573 37230 38 38 116949432 116949432 116949432 111039309 111039309 4900774060 65305944: 27 27 115231456 115233456 115233456 107690629 107690629 4337237928 576239902 30 30 100096806 100096806 100096806 94994021 94994021 3766500235 499721753 32 32 117336764 Ϊ ^"17336764 117336764 110829132 110829132 4318198382 572831174 24 24 107969688 307969688 307969688 103124073 103324073 4384838477 581537935 39 39 116390402 ΪΪ6390402 3 16390402 1 30328368 110328368 4995334492 663307556 33 33 103325630 103325630 303325630 98401082 98401082 4424549836 587707697 26 26 844673 70 84467170 84467170 8043 8228 8043 82.2.8 3395592865 450900028 34 34 123353 2.86 3 2.1351286 3 21351286 3 34213252 1 3423 32.52 4540622894 603567799 31 33 108727236 308727236 308727236 102923099 102923099 4193062181 555933050 35 35 108230704 308230704 308230704 303046592 103046592 4457383691 59108228 1 35 35 114228854 114228854 114228854 108957045 108957045 4843968373 642272572 36 36 117825302 117825302 117825302 111111229 111111229 4512527673 601050053 17 17 ' 72000422 72000422 72000422 68801514 ' 68801514 2947894213 390951044 34 34 88722638 88722638 88722638 84687089 84687089 3663775622 485847315 3831 1831 122281924 122281924 122283924 120727881 120727883 7643188181 1022494336 2395 2395 162352944 162352944 162352944 160600863 160600863 9970296070 1333793927 2310 2310 1590901 38 1590903 18 1590903 3 8 157275770 157275770 9816595203 1334029518 2444 2444 167119230 1673 39210 1671 39230 165258539 165258539 302.97235070 1376796519 21 28 2128 153514804 153534804 153534804 151537565 151537565 9380809913 1254588930 3742 1742 119338904 119338904 119338904 117899079 117899079 7491598339 1002745541 2266 2266 161604944 161604944 161604944 159788630 159788630 9891132806 1323353122 2143 2143 146227460 ^"146227460 146227460 144441120 144441120 8884157225 ΙΪ88799573 1966 3966 137549296 337549296 337549296 136026866 136026866 8412506409 112535466 PF Reads PF Unique PF Unique

PF Noise PF Noise PF Reads PF Reads Aligned PF Reads Bases Reads

Reads AP Reads PF Reads AP Al HS AP Aligned Aligned Aligned

694 2033 2033 141724660 141724660 141724660 140256753 140256753 8672943785 115990086

695 2100 2100 144989780 144989780 144989780 143480396 143480396 8964193868 119945822

696 2226 2226 156025412 156025412 156025412 154381161 154381161 9549714668 127742636

697 2336 2336 158560902 158560902 158560902 156868137 156868137 9559775102 127876840

698 1648 3648 112270114 Ϊ Ϊ2270Π4 3 12270114 1 30963472 110963472 7022034557 93971864

699 206 2064 142548062 3 42548062 342548062 140939826 140939826 8659450614 115845714

700 1676 3676 116509834 116509834 3 16509834 1 35321677 115321677 7324405568 98023532

70S 11338 3 3338 133372108 3 33372108 333372108 333699258 133699258 5943880843 78816192

702 14972 34972 175343340 3 75143340 375143340 373463946 173463946 8135424549 308041497

703 13659 33659 160237664 360237664 360237664 158509770 158509770 8134574392 308262136

704 5541 5541 218698480 218698480 23 8698480 230077287 210077287 4349764229 58592620

705 4248 4248 162700558 362700558 362700558 160665314 160665314 7086299053 94582808

706 4269 4269 163150662 163150662 163150662 154429935 154429935 4680356999 63670458

707 5749 5749 ' 239881506 239881506 239881506 222122888 ' 222122888 1853758055 26174826

708 4979 4979 201171882 201173882 201173882 183676773 183676773 3894822097 53356380

709 5027 5027 197574004 197574004 197574004 185989234 185989214 5415918756 73333840

710 4617 4617 185629188 1856293 88 1856293 88 178384643 178384643 3646672698 49023841

711 3208 3208 120197600 120397600 120197600 118795627 118795627 508017999 6764948

712 4897 4897 188193506 188393506 188193506 183083002 183083002 5010579433 67305468

713 41 53 4153 168322434 168322434 168322434 165908728 165908728 6391174790 85467579

714 3365 3365 118317778 118337778 118317778 117202890 117202890 6000299081 80222630

715 4291 4291 153829666 153829666 153829666 152677841 152677841 7461068776 99660131

716 3456 3456 129195016 129195016 129195016 127891830 127891830 6316338499 84583016

717 3804 3804 146246272 ^"146246272 146246272 144623968 144623968 6848746508 9Ϊ606596

718 3328 3328 125006072 Ϊ 25006072 325006072 123769141 123769141 6294267807 84170495

719 3717 3717 1323 11574 132111574 332111574 130955025 130955025 6180883387 82583730

720 4134 4334 1699802.92 369980292 369980292 3673 77256 167377256 651 3830774 87063909

721 3840 3840 1508782.78 3 50878278 3 50878278 3493 75561 149375561 6883603 858 92.005728

722 3898 3898 149533144 349533144 349533144 348089328 148089328 6893267808 92.108382

723 1085 Ϊ 30851 112006634 3 12006634 3 3 2006634 1 30240672 110240672 7074497059 94063952

724 12770 32770 139496110 3 39496110 339496110 137972150 137972150 8528005752 3 13332487

725 12426 12426 136546934 136546934 136546934 134233606 134233606 8593944618 114327496

726 Ϊ39Ϊ7 13917 ' Ϊ50869Ϊ32 Ϊ50869Ϊ32 150869132 147917630 ' Ϊ479Ϊ7630 9683278875 128813797

727 32243 12243 133989852 133989852 133989852 132303753 132303753 8515193638 113126585

728 9447 9447 99002488 99002488 99002488 97547434 97547434 6319593171 84059481

729 32919 12919 140966828 140966828 140966828 139352824 139352824 8729915465 116033558

730 33371 13373 145043938 145043938 145043938 142399422 142399422 9117203797 12335042.8

731 3 3939 11939 128666990 128666990 128666990 126436433 126436433 8264189649 109955757

732 33418 13418 143179610 143179610 143179630 141674053 141674053 8767928386 116523283

733 33220 13220 140904188 1409043 88 140904388 138120998 138120998 8884738348 118229748

734 33987 13987 148776204 148776204 148776204 146903487 146903487 9363285046 124408928

735 12447 12447 147267852 147267852 147267852 142118955 142118955 8973138149 120572764

736 10127 10127 101698236 101698236 101698236 100198491 100198491 6528934454 86834454

737 11650 3 1650 125368206 3 25168206 325168206 123911648 123911648 7873941710 104643 74

738 13998 33998 146358724 3 46158724 346158724 143089543 143089543 9229809699 122848171

739 13381 33381 145813654 145813654 345813654 143096346 143096346 9073873645 120782029

740 15942 3 5942 167573 124 367571124 367571124 363368837 163368837 10494532.510 3 39708033

741 12987 3 2987 1378332.92 3 37833292 337833292 3363 10539 1363 30539 8572708061 3 14012516

742 13663 33661 142875926 342875926 342875926 143294768 143294768 8841773597 3 17495861

743 12358 32358 137253106 3 37253106 337253106 135480641 135480641 8513806292 3 13178837

744 10624 10624 114624812 114624812 114624812 113613813 113613813 7308951030 97087252

745 10376 10376 105853004 105853004 105853004 103652686 103652686 6734126960 89606839

746 13583 13583 ' Ϊ46476322 146476322 146476322 144848423 ' Ϊ448 8423 8899677777 118249804

747 32326 12326 131166200 131166200 131166200 129589227 129589227 8112032107 107793031

748 33999 13999 14 732684 149732684 149732684 146567541 146567543 9358651456 124484503

749 30609 10609 135735808 135735808 135735808 133356878 133356878 8679124634 115504861

750 33058 13058 136591968 136593968 136593968 134237872 134237872 8630249512 114763934

751 30498 10498 107055634 107055634 107055634 106006682 106006682 6862528560 91 367925

752 3 3 523 11523 124306000 124306000 124306000 122520632 122520632 7646026666 10173 5704

753 30566 10566 108678172 1086783 72 108678372 107187258 107187258 6884798846 91536534

754 11954 11954 131119220 131119220 131119220 128425124 128425124 8009713217 106590157

755 8994 8994 94530862 94530862 94530862 93513609 93513609 6003947037 79793652

756 12353 32353 134822768 334822768 334822768 132721558 132721558 8189246263 108833871

PF Reads PF Unique PF Unique

PF Noise PF Noise PF Reads PF Reads Aligned PF Reads Bases Reads

Reads AP Reads PF Reads AP Al HS AP Aligned Aligned Aligned

820 13097 13097 159189366 159189366 159189366 155766746 155766746 30442734068 139120520

82 i 16231 16231 203393568 203393568 203393568 193476854 193476854 3 2370862988 165893 393

822 17493 17493 215547998 215547998 215547998 210723243 210723243 12216377261 162954047

823 9790 9790 121308398 121308398 121308398 119120642 119120642 7697318057 ^"102545748

824 15271 35271 189363092 Ϊ 89163092 389163092 186827473 186827473 11333 327909 150680191

825 12643 32643 153734980 153734980 353734980 149746659 149746659 10024547018 133690845

826 12688 32688 182831968 182831968 382831968 178294553 178294553 11845218388 157884003

827 12556 3 2556 153486370 3 51486370 3 51486370 348963801 148963801 9782668760 3 30248689

828 15128 3 53 28 184769782 3 84769782 3 84769782 379813496 17983 3496 11889700291 3 58756927

829 13550 33550 165024614 365024614 365024614 162004842 162004842 10747397574 343003554

830 13174 333 74 163320496 363320496 363320496 160474601 160474601 10443038576 3 39050556

83 i 9483 9483 138048392 3 38048392 338048392 135639708 135639708 8955886434 3 19224186

832 14191 14191 174617142 174617142 174617142 171193536 171193536 10023845377 133808384

833 Ϊ6352 16352 ' 203301626 20330Ϊ626 203301626 198703864 ' Ϊ98703864 13078790849 174714415

834 34133 14133 176924158 l^" 769243 58 176924358 169147333 169147333 11174322626 149145186

835 36366 16366 202523832 202523832 202523832 197319163 197319163 12909258574 172090841

836 34504 14504 184351356 184353356 184353356 177415649 177415649 3 1056595664 1483 3 5986

837 3 3 577 11577 143786050 143786050 143786050 142004903 142004903 9134570950 123582580

838 3 5137 15137 193261408 193263408 193263408 189785784 189785784 3 1875064533 158348459

839 30788 10788 134474470 134474470 134474470 133096463 133096463 8275021896 110126310

840 30847 10847 155748398 155748398 155748398 148073996 148073996 9706895173 129943865

841 15530 15530 188735806 188735806 188735806 184878029 184878029 11766589794 156755136

842 12209 12209 148476270 148476270 148476270 145362045 145362045 9645967795 128509653

843 13019 13019 160466436 ^"166466436 160466436 156178957 156178957 10348875327 137918155

844 9239 9239 112214174 3 ^"1221 1^" 74- 3 12214174 95380739 95380739 6277237817 83729875

845 12505 32505 152016730 152016730 352016730 148599124 148599124 9702234193 129289497

846 9132 9332 1 33239770 3 13239770 3 3 3239770 3 30767243 1 30767243 7099446862 94498191

847 11102 3 3 302 137063 728 3 37061728 337061728 329548967 129548967 8657963 762 3 15485487

848 12173 3 23 73 155458408 3 55458408 3 55458408 345541059 145541059 9063993620 3 22098265

849 13216 33216 162084136 362084136 362084136 158097272 158097272 10438320578 3 39209407

850 8524 8524 106209692 306209692 306209692 104682906 104682906 6866849378 91418658

851 12845 12845 158610422 158610422 158610422 155673179 155673179 10075583536 134062883

852 12486 12486 ' Ϊ49802318 Ϊ498023Ϊ8 149802318 145357487 ' Ϊ45357487 9487023195 126615084

853 36159 16159 201594180 2015943 80 201594380 194500691 194500693 11699959703 156789192

854 33740 13740 168249532 Ϊ68249532 168249532 162925889 162925889 10326899212 138060320

855 34897 14897 179599028 179599028 179599028 161442585 161442585 6394012076 85147741

856 3 5227 15227 186230232 186230232 186230232 171863627 171863627 7386742833 98402654

857 3 5586 15586 193807786 193807786 193807786 171970948 171970948 6396259942 85409873

858 32943 12943 152414166 152434366 152414366 144437043 144437043 7232192546 96337473

859 32893 12893 192977226 192977226 192977226 184464493 184464493 7926098058 105525227

860 33829 13829 175171138 175173 3 38 175173 338 17273363 5 172733615 30320416756 137538364

861 6693 6693 92337360 92337360 92337360 59951872 59951872 48526719 745788

862 16022 16022 232071366 232071366 232071366 220616574 220616574 10595564358 ^"141238410

863 917 937 168855700 Ϊ 68855700 368855700 167731517 167731517 9904654446 131484661

864 800 800 154382754 Ϊ 54182754 354182754 153206346 153206346 9071 384474 120496329

865 927 927 178309054 178109054 378109054 176869094 176869094 10002256772 132713276

866 904 904 169837176 369837176 369837176 368453603 168453603 9969250352 3 32393042

867 619 639 1 39542190 3 19542190 3 39542190 3 3 8560047 1 38560047 7058583534 93765529

Penalty

20x of QC QC QC QC

Pa r XX Catch Catch Catch Pond

PF Unique Orientation Penalty Penalty Picard Penalty Penalty Penalty Pico Pico Pico Pico Reads INS iOOX 10x ^" Data 30x 40X 50X Quant Row Well Column

1 130556807 F 5.83787 4.26 4.37 4.51 4.64255 4.8016 8,64 C C01 1

2 124215084 FR 5.6262 4.36 4.47 4.58 4.68971 4.81755 8,98 D D01 1

3 124294096 FR 6.88018 4.57 ' 4.72 4.89 5.07852 * 5.28532 8,15 E ' E01 1

4 120205114 FR 5.90674 4.36 4.48 4.61 4.74461 4.89188 10.05 II HOI 1

5 118497476 FR 6.06339 4.33 4.46 4.59 4.74417 4.9101 8.38 c C02 2

108753451 FR 5.92324 4.39 4.5 4.63 4.76929 4.91797 8.98 _D , D02 2 η 116019049 FR 5.6674 4.36 4.46 4.58 4.69427 4.82935 9.26 G G02 2

8 97638724 FR 6.33373 4.45 4.59 4.73 4.88684 5.06085 9.8 A A03 3

9 113765864 FR 6.03237 4.5 4.62 4.75 4,88508 5.03658 8.87 B B03 3 i O 102938451 FR 6.12389 4.4 4.53 4.67 4,81386 4.98533 9.69 C C03 3

11 121138946 FR 8.82447 4.95 5.16 5.4 5,69203 6.00397 7.6 D D03 3

12 117087933 FR 5.93718 4.34 4.46 4.58 4,72997 4.88569 8.87 E E03 3

13 96074325 FR 7.81275 5.11 5.29 5.48 5.6949 5.94022 9.2 F F03 3

14 120327587 FR 6.62046 4.7 4.84 4.99 5.15852 5.33924 9.04 G G03 3

15 110773194 FR 5.83948 4.31 4.43 4.55 4.7046 4.84904 8.97 II II03 3

16 1 21001071 FR 8.7339 5.17 5.37 5.6 5.8635 6.3543 7 9.04 B B04 4

17 1 17033898 FR 7.8756 4.72 4.93 5.12 5.34329 5.60665 8.47 C C04 4

IS 1 14879032 FR 6.74242 4.52 4.67 4.83 5.01688 5.22571 8.21 D D04 4

1 1 20618074 FR 7.13514 4.97 5.13 5.29 5.48226 5.6843 2 8.8 G G04 4

20 104447405 FR 6.0486 4.36 4.49 4.63 4.77012 4.93644 8.63 B B05 5

21 119715875 FR 6.07176 4.4 4.53 4.67 4.81041 4.97646 10,22 D DOS 5

22 119207298 FR 7.50809 5.Ϊ9 ' 5.36 5.53 5.73089 ' 5.94232 8,3 E ' E05 5

23 104591453 FR 7.16595 4.96 5.12 5.29 5.47128 5.68157 9.21 F F05

24 104435892 FR 8.02232 5.41 5.59 5.79 5.99455 6.2361 9.81 A A06 6

25 108056231 FR 8.95061 5.41 5.62 5.85 6.11984 6.41213 8.98 B B06 6

26 105868414 FR 7.07336 4.93 5.07 5.25 5.35463 5.5705 8.49 C C06 6

27 109625423 FR 5.98225 4.34 4.46 4.6 4.74672 4.89688 8.73 D D06 6

28 104627095 FR 5.8988 4.38 4.5 4.63 4,75781 4.91093 8.62 F F06 6

29 126194444 FR 7.32679 4.38 4.56 4.75 4,96932 5.21365 8.39 G G06 6

30 125473232 FR 7.28659 4.45 4.62 4.81 5,02298 5.25715 9.11 H H06 6

31 103250793 FR 9.60595 4.87 5.09 5.35 5,63846 5.98324 8.25 A A07 7

32 ΙΪ3268574 FR 6.Ϊ4383 4.35 4.47 4.61 4,77063 4.94419 8.62 B B07 7

33 115709586 FR 7.32048 4.36 4.53 4.73 4.94143 5.18836 8.24 D D07 7

3 114012049 FR 10.88473 4.86 5.1 3 5.38 5.70648 6.10386 7.51 E E07 7 5 1 1638111 1 FR 8.13616 4.26 4.45 4.67 4.92169 5.20906 8.3 5 A AOS 8

36 1 28140107 FR 9.54665 5.1 5.32 5.58 5.87437 6.2364 8.53 B BOS 8

37 1 11743959 FR 6.4516 4.43 4.57 4.73 4.90177 5.08863 8.35 C COS 8

38 1 18342644 FR 7.28439 4.45 4.62 4.81 5.02655 5.263 55 7.66 E E08 8

39 1 37546767 FR 6.10196 4.26 4.39 4.54 4.69407 4.8694 8.46 F F08 8

40 114375745 FR 12.58173 5.36 5.63 5.95 6.31594 6.75032 8,34 G G08 8

41 112870666 FR 6.96955 4.33 ' 4.49 4.67 4.87998 ' 5.09712 9,24 II ' H^"08 8

42 109376156 FR 9.39933 4.59 4.81 5.06 5.34323 5.68434 8.62 A A09 9

43 119624569 FR 15.75538 5.25 5.55 5.89 6.29389 6.78822 8.47 C C09 9

44 110638718 FR 6.29039 4.31 4.44 4.59 4.76228 4.93931 9.75 Ό D09 9

45 103728522 FR 7.2053 2 4.82 4.98 5.16 5.35655 5.57301 8.69 E E09 9

46 105795412 FR 7.68876 5.03 5.19 5.38 5.59574 5.84406 8.54 F F09 9

47 1066261 71 FR 6.46325 4.4 4.55 4.7 4,87213 5.06515 9.27 G G09 9

48 108205547 FR 6.0773 4.36 4.49 4.62 4,77508 4.93363 9.85 H H09 9

49 988791 58 FR 6.14989 4.43 4.54 4.68 4,8268 4.9957 9.92 A A30 10

50 104202390 FR 6.34745 4.37 4.51 4.66 4,82157 5.01577 9.63 B BIO 10

51 104779282 FR 6.26973 4.33 4.47 4.61 4,77905 4.96172 8.82 C CIO 10

52 106581553 FR 6.06891 4.4 4.53 4.66 4.80656 4.96387 9.59 D D10 30

53 106707905 FR 6.23303 4.41 4.54 4.69 4.83587 5.03406 8.28 E EiO 30

5 107288821 FR -1 5.26 5.66 6.18 6.82903 7.74006 8.39 F F30 30

55 i 14241441 FR 9.22557 4.81 5.02 5.27 5.55257 5.8783 8 9.47 G G10 30

56 3 15403402 FR 7.07285 4.55 4.72 4.9 5.09107 5.33764 9.74 H HtO 30

57 3 14414905 FR 8.07272 4.71 4.93 5.12 5.36143 5.6388 30.27 A Al l 3 3

58 97175435 FR 30.23941 5.22 5.47 5.74 6.04913 6.43393 9.62 B Bl l 3 3

59 92217452 FR -1 6.42 6.89 7.44 8.15701 9.10374 9,58 C Cl l 11

60 95231797 FR -1 4.21 4.46 4.77 5.13727 5.59383 9,01 D Dl i 11

61 59314625 FR -1 12.21 ' -i -1 -i ' -Ϊ 9,27 E ' El l 11 Penalty

20x of QC QC QC QC

Pa r XX Catch Catch Catch Pond

PF Unique Orientation Penalty Penalty Picard Penalty Penalty Penalty Pico Pico Pico Pico Reads INS iOOX lOx Data 30x 40.X 50X Quant Row Well Column

62 86074161 F 7.35623 4.31 4.48 4.68 4.8925 5.14797 11,08 B B01 1

63 94399893 FR 6.59508 4.39 4.55 4.71 4.89374 5.08898 11,81 C C01 1

64 84954872 FR 5.78301 4.44 ' 4.54 4.66 4.78513 ' 4.92103 12,29 A ' A02 2

65 96573116 FR -3 35.17 45.92 85.19 -1 -1 11.17 Ft B02 2

66 96863389 FR -3 43.64 78.45 -3 -1 -1 9.86 C C02 2

67 98598140 FR 5.74701 4.5 4.6 4.73 4.82.768 4.95511 13.5 _D , D02 2

68 100040507 FR 5.6433 2 4.48 4.57 4.68 4.79383 4.90461 11.74 E E02 2

69 87579094 FR 5.83405 4.47 4.58 4.69 4.82.2.85 4.95755 12.3 G G02. 2

70 91087285 FR 5.71302 4.44 4.54 4.65 4,77363 4.90126 12.16 H H02 2

71 87792228 FR -3 5.37 5.75 6.55 7.75542 10.06076 8.95 B B03 3

72 61366397 FR -1 4.33 4,8 5.44 6,37923 8.08658 12.71 A A04 4

73 133030499 FR 10.21913 ' 7.98 8.17 8.36 8,56586 8.79532 7.66 B B01 1

74 62781927 FR 8.57172 6.52 6.68 6.85 7.04218 7.24215 8.58 C C01 3

75 129052535 FR 9.31665 7.19 7.37 7.55 7.7443 7.94737 7.07 D D01 3

76 121619370 FR 5.79102 4.5 4.6 4.72 4.83872 4.96342 9.65 C C01 3

77 1 23760707 FR 6.64246 4.87 5.03 5.15 5.30755 5.47552. 9.79 D DO 3 3

78 1 2.3243817 FR 5.66271 4.35 4.45 4.56 4.68558 4.82267 8.03 F F03 3

79 1 15584569 FR 6.91445 4.91 5.05 5.21 5.38542 5.57724 7.98 H HO! 3

80 109356750 FR 6.1275 4.69 4.8 4.92 5.04986 5.19738 9.84 A A02 2

81 1 6629422 FR 6.12985 4.69 4.83 4.93 5.05876 5.2043 5 9.43 B B02 2

82 121986750 FR 5.62559 4.3 4.41 4.52 4.64488 4.77506 9,11 c C02 2

S3 112674860 FR 6.38222 4.6 ' 4.74 4.88 5.03254 ' 5.20393 9,54 D ' D02 2

84 113882905 FR 5.93361 4.46 4.57 4.7 4.82914 4.97899 7.86 E E02 2

85 116085326 FR 5.80954 4,45 4.56 4.68 4.79933 4.93322 9.6 11 H02 2

86 119335112 FR 5.69739 4.36 4.47 4.58 4.70739 4.84118 9.31 B B03 3

87 10882852.0 FR 5.82936 4.34 4.46 4.58 4.71838 4.85885 10.32 C C03 3

88 14577489 FR 6.23607 4.48 4.61 4.75 4.89991 5.06898 8.92 D D03 3

89 1192121 54 FR 5.90307 4.43 4.54 4.66 4,79961 4.94082 9.97 A A04 4

90 1120541 24 FR 6.16702 4.64 4.77 4.89 5,03631 5.18516 9.73 B B04 4

91 99858664 FR 7.11412 4.9 5.06 5.23 5,40998 5.61893 9.05 C C04 4

92 101010905 FR 6.02095 4.52 4.63 4.76 4,89846 5.03964 8.71 D D04 4

93 ΙΪΪ329855 FR 6.06161 4.43 4,56 4.69 4,84083 4,99869 8.8 F F04 4

94 121437307 FR 5.80992 4.4 4.53 4.63 4.75772 4.8962 9.01 G G04 4

95 107675870 FR 5.95382 4.44 4.56 4.68 4.82362 4.97256 9.38 H 1104 4

96 1 11397066 FR 5.87348 4.53 4.64 4.76 4.88026 5.03699 9.66 A AOS 5

97 106805409 FR 6.2.7539 4.69 4.83 4.94 5.091 37 5.2435 8.75 B BOS 5

98 109548016 FR 6.1464 4.43 4.56 4.7 4.84538 5.03042 9.1 C COS 5

99 1 17022501 FR 6.9684 4.67 4.83 4.99 5.18245 5.39859 9.48 D D05 5

100 1 23069901 FR 5.90327 4.41 4.53 4.66 4.78615 4.93901 8.4 E E05 5

101 114862512 FR 5.76452 4.34 4.46 4.58 4.70822 4.84128 9,36 F F05 5

102 127754811 FR 8.71451 5 ' 5.21 5.45 5.70642 ' 6.60806 8,4 G ' G05 5

103 101459394 FR 6.1329 4.64 4.76 4.88 5.02196 5.17009 10.35 A A06 6

104 117131308 FR 5.92239 4.36 4.47 4.6 4.74785 4.89081 9.08 B B06 6

105 113030478 FR 5.593 35 4.42 4.52 4.63 4.73591 4.85289 8.33 D D06 6

106 114161791 FR 6.20597 4.67 4.79 4.92 5.0551 5.21033 8.45 E E06 6

107 113407536 FR 5.8964 4.36 4.48 4.6 4.73802 4.88701 7.8 F F06 6

108 196739710 FR 5.93737 4.33 4.46 4.59 4,72839 4.88609 8.4 G G06 6

109 112163142 FR 5.94659 4.45 4.57 4.69 4,82934 4.97325 8.91 H H06 6

1 10 102714765 FR 6.14563 4.43 4.55 4.69 4,83575 5.00159 9.57 A A07 7

111 115524944 FR 6.13107 4.52 4.64 4.78 4,91716 5.08356 7.94 B BO 7 7

112 ^"101086670 FR 6.86635 4.86 5.01 5.17 5,33744 5.53237 7.43 D D07 7

113 95107832 FR 6.26504 4.47 4.6 4.75 4.90287 5.07093 7.38 E E07 7

114 111767591 FR 6.03442 4.38 4.5 4.63 4.78159 4.93969 9.78 G GO 7 7

115 118829627 FR 5.89443 4.4 4.52 4.64 4.77723 4.92514 30.26 H 1107 7

116 1 17913209 FR 5.94544 4.39 4.53 4.64 4.7758 4.93081 9.52. A AOS 8

117 102044108 FR 6.40703 4.48 4.62 4.77 4.93929 5.3 3 396 7.51 B BOS 8

118 122477772 FR 5.96701 4.33 4.45 4.59 4.73475 4.88358 7.49 C COS 8

119 1 15679495 FR 5.9683 4.44 4.55 4.68 4.81972 4.96432 9.53 D DOS 8

120 112817224 FR 5.98675 4.34 4.46 4.59 4.74432 4.90029 8,32 E EOS 8

121 123132301 FR 6.04843 4.4 4.52 4.66 4.80461 4.95731 8,06 F F08 8

122 103743011 FR 6.25085 4.48 ' 4.61 4.75 4.90191 ' 5.07023 9,79 G ' GOS 8 Penalty

20x of QC QC QC QC

Pa r XX Catch Catch Catch Pond

PF Unique Orientation Penalty Penalty Picard Penalty Penalty Penalty Pico Pico Pico Pico Reads INS iOOX 10x ^" Data 30x 40X 50X Quant Row Well Column

123 108438919 F 6.03242 4.41 4.54 4.67 4.81662 4.96764 9,89 H H08 8

124 105320960 FR 5.93177 4.45 4.56 4.69 4.82674 4.97342 9,06 A A09 9

125 122271115 FR 5.85466 4.38 ' 4.48 4.61 4.74693 ' 4.89268 8,76 c ' C09 9

126 108839669 FR 5.86393 4.41 4.52 4.65 4.77672 4.92337 9.22 D D09 9

127 109088040 FR 5.99388 4.35 4.48 4.62 4.7616 4.91668 9.38 E E09 9

1 28 19649495 FR 11.31 1 21 7.3 8 7.44 7.74 8.05218 8.42644 8.94 _F F09 9

1 29 107433784 FR 7.5239 5.05 5.21 5.4 5.60627 5.82159 10.3 H H09 9

1 0 107045163 FR 6.4351 8 4.83 4.95 5.08 5.23487 5.38584 8.99 A AJ 0 10

1 31 91981497 FR -1 -1 -1 -3 -i -1 7.34 C C30 10

1 32 109085532 FR 6.62698 4.52 4.67 4.82 5.0014 5.20296 8.57 D D10 10

133 64046235 FR -1 - 1 -1 -1 -1 -1 1.8 E E10 10

134 97722411 FR -Ϊ - 1 -1 -Ϊ -1 -1 3.94 F F10 10

135 62550022 FR -1 - 1 -1 -1 -1 -1 2.44 G G10 30

136 75722934 FR -1 - 1 -1 -1 -1 -1 6.08 H H10 30

137 127251302 FR 6.50752 4.74 4.88 5.02 5.17292 5.34433 30.16 A Al l 3 1

138 1 16526692 FR -1 4.64 4.93 5.29 5.73065 6.28638 7.39 C CI I 3 3

139 109900744 FR 7.55171 5.5 5.66 5.82 5.99925 6.39957 8.96 D D1 3 3 3

140 108202859 FR 6.20313 4.57 4.69 4.83 4.9701 5.134 8.91 E El i 3 3

141 1 15092856 FR 5.73921 4.34 4.45 4.56 4.68923 4.83227 30.39 F F3 3 3 3

142 36913155 FR -1 7.86 -3 -1 -1 -3 6.73 G Gi l 3 3

143 49417027 FR -1 5.77 -1 -1 -1 -1 7,62 H Hl l 11

144 112742014 FR -1 4.64 ' 4.92 5.27 5.69918 * 6.23429 8,39 A ' A12 12

145 114391628 FR 7.59291 5.69 5.84 6 6.17628 6.35882 9.63 B B32 12

146 119988237 FR 5.8607 4.6 4.7 4.82 4.93661 5.06388 8.68 C C32 12

147 124442316 FR 5.49387 4.31 4.4 4.52 4.62233 4.74488 9.51 D D12 12

148 33869883 FR -3 8.41 -1 -3 -i -1 7.8 E El 2 12

149 27506406 FR -3 8.24 -1 -3 -i -1 8.02 F F12 12

1 50 111010075 FR 8.93364 4.55 4.75 4.99 5.26554 5.58469 12.72 B B03 1

1 51 84164255 FR 6.65538 4.53 4.66 4.82 4,99833 5.19829 12.07 C CO 3 1

152 133735832 FR 6.77042 4.46 4.62 4.79 4,97781 5.18485 12.68 D DO! i

153 114984050 FR 6.86241 4.5 4.66 4.84 5,02532 5.23073 12.57 E E01 i

154 ΙΪ8926421 FR 6.73375 4.42 4.58 4.74 4,93251 5.13265 12.86 F F01 i

155 122559630 FR 6.45615 4.4 4.54 4.7 4.87246 5.05257 32.79 G GO I 3

156 221778146 FR 6.25915 4.28 4.42 4.57 4.73233 4.93671 33.28 H 110 Ϊ 3

157 1 19772761 FR 7.96623 4.79 4.98 5.19 5.42459 5.69465 3 2.53 A A02 2

158 1 25791898 FR 6.76316 4.4 4.56 4.73 4.90932 5.32976 3 2.32 B B02 2

159 80976245 FR 1 5.68437 4.44 4.7 4.99 5.34492 5.7904 3 2.29 C C02 2

160 1 14828104 FR 7.01125 4.43 4.59 4.78 4.97645 5.20647 32.76 D D02 2

161 1 3345981 FR 6.96951 4.46 4.62 4.8 4.99044 5.23606 33.49 E E02 2

162 121457661 FR 6.60322 4.39 4.54 4.7 4.88541 5.09018 13, 11 F F02 2

163 119092002 FR 7.01858 4.46 ' 4.62 4.81 5.00138 * 5.22414 13,83 G ' G02 2

164 123176054 FR 6.54805 4.37 4.51 4.68 4.86089 5.05117 12.07 B B03 3

165 115969632 FR 7.03725 4.48 4.64 4.81 5.01204 5.24366 13.22 C C03 3

166 125741403 FR 6.81551 4.32 4.48 4.66 4.85254 5.06917 12.25 D D03 3

167 121890621 FR 6.65327 4.33 4.48 4.65 4.83027 5.03965 13.29 E E03 3

168 10091 1340 FR 7.09433 4.53 4.69 4.88 5.07834 5.30455 13.63 F F03 3

169 133132208 FR 6.65553 4.36 4.51 4.68 4,86659 5.07165 12.77 G G03 3

1 70 122254423 FR 6.94963 4.48 4.64 4.82 5,00752 5.23034 13.66 H H03 3

1 71 70072763 FR 16.00181 4.62 4.88 5.18 5,5549 6.0073 12.74 A A04 4

172 124935509 FR 7.02432 4.44 4.6 4.77 4,97956 5.20822 12.38 C C04 4

173 93871675 FR 7.58908 4.49 4.67 4.88 5,09236 5.35224 13.29 D D04 4

174 109393602 FR 7.10175 4.46 4.63 4.81 5.00687 5.23717 33.75 E E04 4

175 121238242 FR 6.59318 4.38 4.52 4.68 4.85944 5.05901 32.63 F F04 4

176 129667172 FR 7.76994 4.58 4.78 4.97 5.21117 5.47227 32.3 G CW4 4

177 1 21709732 FR 7.18087 4.68 4.84 5.03 5.21775 5.44273 33.2 H H04 4

178 1 11493183 FR 6.26262 4.42 4.56 4.7 4.85638 5.03792 3 2.18 A AOS 5

179 1 12341499 FR 7.69608 4.68 4.86 5.06 5.28569 5.53949 33.28 C C05 5

ISO 1 4679305 FR 6.67544 4.41 4.57 4.73 4.91075 5.1 3969 32.88 D DOS 5

181 128493012 FR 6.6867 4.35 4.5 4.68 4.86088 5.07279 12,42 E EOS 5

182 113890135 FR 6.50516 4.4 4.54 4.71 4.87323 5.06472 13,74 F F05 5

183 193427090 FR 6.32218 4.33 ' 4.47 4.62 4.79ΪΪ ' 4.97276 13,69 G ' G05 5 Penalty

20x of QC QC QC QC

Pair XX Catch Catch Catch Pond

PF Unique Orientation Penalty Penalty Picard Penalty Penalty Penalty Pico Pico Pico Pico Reads INS iOOX 10x ^" Data 30x 40X 50X Quant Row Well Column

184 115065946 F 7.12142 4.52 4.68 4.88 5.07335 5.30352 12, 13 A A06 6

185 116862380 FR 7.66657 4.61 4.79 4.99 5.21364 5.47808 12,58 B B06 6

186 115548398 FR 7.50402 4.54 ' 4.72 4.92 5.13549 ' 5.396 11,7 c ' C06 6

187 130777445 FR 6.57539 4.49 4.63 4.78 4.95758 5.14929 12.46 Ό D06 6

188 1081 36264 FR 7.70201 4.59 4.77 4.97 5.19278 5.45198 13.26 E E06 6

1 89 100588195 FR 10.63682 4.65 4.88 5.16 5.47863 5.85087 12.44 _F F06 6

190 216120355 FR 6.32567 4.33 4.47 4.62 4.78435 4.96805 12.96 G G06 6

191 121709031 FR 6.95627 4.4 4.56 4.74 4.94697 5.17023 13.34 H H06 6

192 103409698 FR 7.27532 4.55 4.72 4.91 5.3 2052 5.35994 11.67 A A07 7

193 123045833 FR 7.17326 4.5 4.67 4.85 5.05283 5.28986 11.69 B B07 7

194 116770828 FR 8.55607 4.6 4.8 5.03 5,2969 5.59376 12.21 C CO 7 7

193 117016065 FR 7.64438 4.53 4.71 4.91 5,13644 5.39737 12.05 D D07 7

196 110953552 FR 6.67097 4.51 4.66 4.82 4.99132 5.19991 3 1.8 E E07 7

197 201123881 FR 6.68466 4.35 4.5 4.66 4.85949 5.06808 32.84 G GO 7 7

198 116806561 FR 7.56974 4.76 4.93 5.13 5.34667 5.59631 32.64 H II07 7

199 1 17057950 FR 6.99165 4.46 4.62 4.79 4.99863 5.23738 3 2.8 A AOS 8

200 1 24740851 FR 9.95872 5.05 5.28 5.55 5.85797 6.20676 3 2.7 B BOS 8

201 1 19859139 FR 7.9819 4.49 4.68 4.89 5.13996 5.4227 33.2 C COS 8

202 1 1772275 FR 7.80795 4.5 4.68 4.89 5.12127 5.3906 33.74 D DOS 8

203 1 19743964 FR 7.25968 4.47 4.64 4.83 5.0428 5.27937 33.98 E EOS 8

204 125077437 FR 7.52383 4.51 4.68 4.88 5.10932 5.36576 14, 13 F F08 8

205 109338903 FR 7.91744 4.81 5 5.21 5.43749 * 5.70574 13,57 II ' H08 8

206 106280838 FR 7.68746 4.52 4.69 4.9 5.12728 5.39362 13.02 A A09 9

207 118786322 FR 7.4123 4.44 4.62 4.81 5.02315 5.27052 13.51 C C09 9

208 120891017 FR 7.24483 4.37 4.54 4.73 4.93979 5.18734 13.65 Ό D09 9

209 114065493 FR 7.8003 2 4.59 4.77 4.98 5.21404 5.47756 12.96 E E09 9

210 78249990 FR -3 4.64 4.96 5.34 5.821 6.45132 14.19 F F09 9

211 116020276 FR -3 4.74 5.09 5.53 6.09581 6.86266 13.9 G G09 9

212 115930343 FR 7.88929 4.72 4.9 5.11 5.34733 5.60865 13.61 H H09 9

213 110173060 FR 7.27151 4.51 4.69 4.87 5,08083 5.31424 13.53 A A10 10

214 116995591 FR 7.48458 4.46 4.64 4.84 5,05095 5.30356 14.04 B B10 10

215 ΙΪ38Ό7657 FR 7.63285 4.42 4.61 4.81 5,03473 5.30599 12.72 C CIO 10

216 118124531 FR 8.44853 4.6 4.8 5.03 5.2874 5.58057 33.76 D D10 30

217 120554011 FR 7.6324 4.52 4.7 4.9 5.12636 5.38771 33.94 E EIO 30

218 1 21297167 FR 7.78859 4.6 4.78 4.99 5.21923 5.48061 34.62 F F30 30

219 1 16652410 FR 8.77446 4.59 4.83 5.04 5.30885 5.62276 34.24 H H10 30

220 65593748 FR -1 4.65 5 5.43 5.98549 6.73261 33.23 A Al l 3 3

221 52522159 FR -1 4.8 5.22 5.77 6.50158 7.5923 7 34,43 B Bl l 3 3

222 1 16748614 FR 8.43872 4.54 4.75 4.97 5.22745 5.5254 33,78 C Cl l 3 3

223 103873872 FR 8.28862 4.51 4.7 4.93 5.17365 5.47301 13,48 D Dl l 11

224 104759044 FR 8.54034 4.55 ' 4.76 4.98 5.24866 ' 5.55239 14,67 E ' El l 11

225 107932555 FR 13.50048 5.05 5.32 5.65 6.00726 6.46347 15.19 F Fl l 11

226 213083920 FR 9.42104 5.2 5.42 5.67 5.96078 6.2899 14.64 G Gi l 11

227 126232488 FR 7.76623 4.58 4.76 4.98 5.20219 5.46743 11.33 A A12 12

228 107285287 FR 7.65478 4.55 4.74 4.93 5.36142 5.41897 14.16 B B3 2 12

229 113680232 FR 7.77493 4.5 4.68 4.89 5.3 2677 5.39038 13.62 C C3 2 12

230 127736598 FR 7.17752 4.43 4.58 4.76 4,97573 5.20659 13.65 D DI2 12

231 117492585 FR 6.70269 4.38 4.53 4.7 4,8862 5.09204 15.31 E E12 12

232 104385886 FR 7.9103 3 4.53 4.7 4.91 5,3 5136 5.42109 14.65 F F12 12

233 229521749 FR 8.72914 5.67 5.87 6.09 6,33169 6.61591 14.09 G G12 12

234 131036587 FR 6.7714 4.44 4.6 4.77 4,95021 5.15716 Ϊ2.2Ϊ H H12 12

235 111036985 FR 4 4.75 5.08 5.51 6.0258 6.72807 30.64 B B01 3

236 115215636 FR 7.55748 4.65 4.83 5.02 5.24952 5.49048 30.91 C C01 3

237 43831722 FR 6.30228 4.81 4.93 5.06 5.18997 5.3433 33.18 D D01 3

238 45718422 FR 5.64326 4.54 4.63 4.73 4.83958 4.953 58 3 2.6 E EOi 3

239 46788601 FR 5.89755 4.65 4.75 4.86 4.981 34 5.30803 3 2.41 F FOi 3

240 1 0876718 FR 6.56929 4.21 4.36 4.52 4.71199 4.92.385 32.35 G GO I 3

241 46901501 FR 6.29635 4.67 4.8 4.92 5.07993 5.2386 33.79 H HOI 3

242 91748946 FR 5.44805 4.35 4.45 4.54 4.64398 4.75647 12,8 A A02

243 117542901 FR 10.06417 4.81 5.04 5.3 5.61049 5.9721 12.94 B B02

244 44439812 FR 6.7623 4.88 * 5.02 5.17 5.3379 ' 5.52101 12,7 c ' C02

Penalty

20x of QC QC QC QC

Pa r XX Catch Catch Catch Pond

PF Unique Orientation Penalty Penalty Picard Penalty Penalty Penalty Pico Pico Pico Pico Reads INS iOOX 10x ^" Data 30x 40X 50X Quant Row Well Column

306 92066245 F 5.62239 4.55 4.64 4.74 4.83735 4.95304 14,71 A A02 2

307 94502242 FR 5.91224 4.67 4.77 4.88 4.99725 5.12552 16,76 B B02 2

308 99590S47 FR 5.63846 4.52 ' 4.61 4.71 4.82423 ' 4.93083 16,5 c ' C02 2

309 109077113 FR 4.99067 4.52 4.56 4.61 4.65754 4.70715 18.26 Ό D02 2

310 108832870 FR 5.64208 4.64 4.72 4.81 4.90845 5.01961 16.86 E E02 2

311 9796191 7 FR 5.08735 4.5 4.55 4.61 4.66887 4.7372 17.23 _F F02 2

3 i 2 98704783 FR 5.3081 2 4.53 4.6 4.67 4.74902 4.83822 18.04 G G02. 2

313 99987641 FR 5.80127 4.61 4.71 4.81 4.92.402 5.0487 17.22 H H02 2

314 90855940 FR 5.97584 4.72 4.83 4.94 5.0525 5.18793 15.13 A A03 3

315 92153054 FR 6.00236 4.66 4.78 4.89 5.01682 5.14864 16.73 B B03 3

316 113328206 FR 5.63529 4.56 4.65 4.75 4,85717 4.95867 16.67 C C03 3

317 106217359 FR 5.05464 4.49 4.55 4.6 4,66262 4.72061 16.79 D D03 3

318 100515364 FR 5.52984 4.55 4.64 4.73 4.81674 4.9231 4 36.8 E E03 3

319 100873007 FR 5.12381 4.52 4.58 4.64 4.70268 4.7641 37.95 F F03 3

320 1 14174240 FR 5.20061 4.62 4.68 4.74 4.79727 4.862 38.17 G G03 3

321 94101293 FR -1 4.67 4.95 5.3 5.69736 6.21707 3 5.11 H H03 3

322 94747567 FR 5.38549 4.44 4.53 4.62 4.70853 4.81 1 87 1 5.31 A A04 4

323 99734546 FR 5.97023 4.71 4.82 4.94 5.04868 5.17125 16,83 B B04 4

324 96123627 FR 5.68275 4.45 4.56 4.67 4.77 1 1 4.90003 16,07 C C04 4

325 1 16005467 FR 5.11157 4.62 4.66 4.71 4.76405 4.81945 17, 18 D D04 4

326 86916026 FR 5.98362 4.61 4.73 4.85 4.9674 5.10303 17, 11 E E04 4

327 102479344 FR 5.17655 4.51 ' 4.57 4.64 4.70664 * 4.77184 17,07 F ' F04 4

328 103562424 FR 5.19602 4.46 4.53 4.6 4.67938 4.7571 17.52 G G04 4

329 98362109 FR 5.89945 4.64 4.75 4.85 4.974 5.09471 16.79 II H04 4

330 93496828 FR 5.83383 4.71 4.82 4.92 5.01685 5.13177 13.32 A AOS

331 95966734 FR 5.81859 4.62 4.72 4.82 4.93413 5.05739 15.92 B BOS 5

332 96188258 FR 5.73713 4.65 4.74 4.84 4.94968 5.05352 16.29 C COS 5

333 11871 1023 FR 5.20566 4.57 4.64 4.69 4,75942 4.82501 17.2 D DOS 5

334 99234566 FR 5.83507 4.69 4.79 4.89 5,00749 5.11739 17.38 E EOS 5

335 103601385 FR 5.2346 4.56 4.62 4.69 4,75936 4.8253 18.35 F F05 5

336 106849021 FR 5.25629 4.54 4.6 4.67 4,73758 4.82048 17.68 G GO 5 5

337 100607608 FR 5.95503 4.66 4.76 4.88 5,00056 5.12705 16.39 H H05 5

338 93922800 FR 6.15046 4.86 4.97 5.08 5.20017 5.333 1 36.69 A A06 6

339 96077648 FR 6.04221 4.74 4.85 4.97 5.09203 5.22279 36.15 B B06 6

340 103628756 FR 5.73907 4.6 4.69 4.8 4.90699 5.02046 3 5.73 C C06 6

341 105516464 FR -1 6.69 7.17 7.76 8.52762 9.57391 36.56 D D06 6

342 92.673718 FR 6.05838 4.6 4.71 4.84 4.97797 5.12259 36.55 E E06 6

343 1 10782531 FR 5.45068 4.51 4.59 4.68 4.77237 4.87306 36,77 F F06 6

344 107603766 FR 5.07933 4.55 4.61 4.66 4.71145 4.77003 17,66 G G06 6

345 100758095 FR 5.8778 4.64 4.74 4.86 4.97361 5.09951 14,62 II H06 6

346 90140315 FR 5.72441 4.56 ' 4.65 4.76 4.86686 ' 4.98647 15,6 A ' A07 7

347 109605250 FR 6.09086 4.66 4.77 4.89 5.02198 5.17468 15.36 B B07 7

348 99894244 FR 5.927 4.73 4.83 4.93 5.04293 5.16534 16.13 C C07 7

349 110532576 FR 5.1788 4.63 4.68 4.74 4.79484 4.85446 16.88 Ό D07 7

350 95539684 FR 6.2222 4.64 4.76 4.9 5.03989 5.19487 15.63 E E07 7

351 11 181 2861 FR 5.22594 4.54 4.61 4.68 4.7451 4.81168 17.53 F F07 7

352 105765320 FR 5.66692 4.75 4.84 4.93 5,01315 5.11192 16.56 G G07 7

353 98873581 FR 5.92458 4.76 4.86 4.96 5,06906 5.19572 10.32 H H07 7

354 95523347 FR 5.53318 4.51 4.6 4.69 4,79252 4.89771 14.71 A A08 8

355 102846426 FR 6.09335 4.65 4.77 4.89 5,01888 5.16357 15.6 B B08 8

356 95642244 FR 6.37676 5.04 5.16 5.28 5,39246 5.53125 16.86 C C08 8

357 110570978 FR 5.29443 4.76 4.82 4.87 4.92393 4.97787 37.64 D D08 8

358 106784563 FR 5.91476 4.62 4.73 4.84 4.96753 5.10005 36.43 E E08 8

359 98808191 FR 5.36252 4.53 4.6 4.68 4.76676 4.85623 38.25 F F08 8

360 1 11396056 FR 5.19893 4.68 4.74 4.79 4.83986 4.9001 3 8.04 G G08 8

361 99660595 FR 5.69085 4.7 4.79 4.88 4.97554 5.08473 36.96 H H08 8

362 86966048 FR 5.78613 4.61 4.71 4.81 4.93015 5.0391 3 5,39 A A09 9

363 97122366 FR 6.15269 4.8 4.91 5.02 5.15583 5.2881 5 37,04 B B09 9

364 96505725 FR 5.9933 4.75 4.85 4.97 5.08136 5.21163 16,89 C C09 9

365 105548713 FR 5.12065 4.63 4.67 4.72 4.7744 4.82907 17,01 D D09 9

366 105401974 FR 5.97001 4.6 ' 4.7 ί 4.83 4.95679 ' 5.08895 16,47 E ' E09 9 Penalty

20x of QC QC QC QC

Pa r XX Catch Catch Catch Pond

PF Unique Orientation Penalty Penalty Picard Penalty Penalty Penalty Pico Pico Pico Pico Reads INS iOOX lOx Data 30x 40X 50X Quant Row Well Column

367 100884965 F 5.37469 4.63 4.7 4.77 4.8518 4.9227 18, 1 F F09 9

368 76805427 FR 7.01302 4.43 4.59 4.77 4.96974 5.19597 11,39 B B01 1

369 75642926 FR 6.47119 4.48 ' 4.62 4.78 4.94546 ' 5.13509 12,43 c ' col 1

370 62460694 FR 5.5548 4.4 4.5 4.6 4.71209 4.82895 13.25 D DO! 1

37i 64989304 FR 5.7422 4.43 4.54 4.65 4.77221 4.90173 12.57 E E01 1

372 73510464 FR 5.71246 4.32 4.43 4.55 4.67981 4.81508 9.81 _F F01 1

373 55771 51 2 FR 5.49098 4.34 4.44 4.53 4.6436 4.76258 13.15 G GO! 1

374 6252371 3 FR 5.79361 4.28 4.39 4.52. 4.65318 4.79853 13.5 H HOI 1

375 78443399 FR 9.91679 5 5.23 5.5 5.79414 6.15312 12.56 A A02 2

376 64918607 FR 6.00559 4.44 4.56 4.69 4,82343 4.9741 13.15 B B02 2

377 67785311 FR 6.12079 4.37 4.5 4.64 4,79519 4.96569 10.93 C C02 2

378 58745302 FR 5.80468 4.42 4.52 4.65 4,76991 4.90668 Ϊ3.77 D D02 2

379 69502948 FR 5.87917 4.35 4.46 4.59 4.72946 4.8767 3 1.86 E E02 2

380 58586364 FR 5.8758 4.41 4.53 4.65 4.78943 4.92393 33.58 F F02 2

381 63756390 FR 6.83672 4.55 4.73 4.87 5.05559 5.26514 33.56 G cm 2

382 3651556 FR -1 -1 -1 -1 -1 -1 5.46 H H02. 2

383 59564212 FR 5.77456 4.35 4.45 4.58 4.70346 4.84592 33.75 A A03 3

384 68546778 FR 5.49615 4.26 4.36 4.47 4.58273 4.7045 32.94 B B03 3

385 71481260 FR 5.92121 4.46 4.57 4.7 4.82649 4.97235 32.59 C C03 3

386 71467697 FR 5.60937 4.31 4.42 4.53 4.64734 4.76978 30.74 D D03 3

387 67420478 FR 5.55734 4.32 4.42 4.53 4.64029 4.76874 12,51 E E03 3

388 67969517 FR 5.48581 4.33 ' 4.42 4.53 4.64042 ' 4.75693 13 F ' F03 3

389 4405272 FR -3 ■1 -1 -3 -1 -1 4.46 G G03 3

390 64913248 FR 5.68788 4.4 4.51 4.62 4.73707 4.86556 14.46 II H03 3

391 69192595 FR 7.09291 4.44 4.6 4.79 4.99205 5.22548 13.24 A A04 4

392 66760509 FR 5.81802 4.42 4.53 4.65 4.77308 4.91428 12.25 B B04 4

393 63650961 FR 6.22527 4.49 4.62 4.76 4.91015 5.07525 11.8 C C04 4

394 63951935 FR 6.45502 4.39 4.53 4.68 4,85896 5.05049 12.33 D D04 4

395 57270604 FR 6.1881 1 4.46 4.6 4.73 4,88902 5.04349 11.59 E E04 4

396 71909530 FR 5.73621 4.34 4.46 4.58 4,6979 4.83473 12.95 F F04 4

397 67313437 FR 5.55982 4.3 4.4 4.51 4,62306 4.75094 13 G G04 4

398 64669255 FR 5.51003 4.36 4.46 4.56 4,66668 4.77791 14.35 H H04 4

399 68402619 FR 5.94029 4.36 4.49 4.61 4.75229 4.9046 32.31 A AOS 5

400 76431625 FR 6.18532 4.37 4.5 4.65 4.80752 4.97299 3 1.99 B BOS 5

401 74840702 FR 6.59618 4.43 4.58 4.74 4.92457 5.1 3798 3 2.26 C COS 5

402 70679704 FR 6.15319 4.41 4.54 4.68 4.82576 5.00368 3 2.58 D D05 5

403 68065622 FR 5.63809 4.35 4.46 4.57 4.68689 4.83674 3 3.98 E EOS 5

404 60712666 FR 5.50594 4.28 4.38 4.48 4.59614 4.72458 32.45 F F05 5

405 68100921 FR 5.97434 4.38 4.49 4.62 4.76772 4.92085 32.07 G G05 5

406 64471803 FR 5.84325 4.39 4.51 4.63 4.76583 4.90337 14,26 II H05 5

407 76154740 FR 13.9308 5.04 ' 5.3 Ϊ 5.63 6.01726 ' 6.47569 11,67 A ' A06 6

408 60508795 FR 5.80848 4.4 4.52 4.64 4.76497 4.90945 12.29 B B06 6

409 67284568 FR 6.05857 4.47 4.59 4.72 4.85958 5.01964 11.75 C C06 6

410 55807726 FR 6.82463 4.55 4.7 4.87 5.05753 5.2572 9.86 D D06 6

411 62691767 FR 5.81425 4.41 4.52 4.64 4.77452 4.90484 12.32 E E06 6

412 54016770 FR 6.38928 4.54 4.67 4.82 4.97946 5.15302 9.17 F F06 6

413 57243029 FR 5.71461 4.46 4.56 4.67 4,78766 4.914 11.45 G G06 6

414 65591863 FR 5.81638 4.33 4.44 4.57 4,70381 4.8469 12.53 H H06 6

415 56620665 FR 6.09484 4.59 4.7 4.83 4,97056 5.12195 12.95 A A07 7

416 80182881 FR 6.77335 4.49 4.64 4.81 4,9966 5.20727 11.24 B B07 7

417 64629679 FR 6.41776 4.44 4.58 4.74 4,90124 5.08275 12.79 C CO 7 7

418 67287687 FR 5.92842 4.45 4.56 4.69 4.8221 3 4.96902 32.36 D D07 7

419 60449229 FR 5.8955 4.41 4.53 4.66 4.79028 4.93934 33.28 E E07 7

420 64365320 FR 5.96247 4.52 4.63 4.75 4.88664 5.03341 32.72 F F07 7

421 67819300 FR 5.64197 4.35 4.45 4.56 4.68029 4.80992 33.49 G G07 7

422 56569867 FR 5.91089 4.55 4.67 4.78 4.90524 5.04434 33.32 H H07 7

423 68224185 FR 6.97211 4.67 4.82 4.99 5.18353 5.39386 3 3 .44 A AOS 8

424 67447733 FR 5.79072 4.33 4.44 4.57 4.69916 4.83786 3 3 .41 B BOS 8

425 67824853 FR 6.27612 4.38 4.52 4.67 4.82772 5.00375 12,07 C COS 8

426 78573066 FR 7.8244 4.55 4.72 4.93 5.17183 5.43504 9,05 D DOS 8

427 64412621 FR 6.081 4.39 ' 4.52 4.66 4.80627 ' 4.96453 11,81 E ' E08 8

Penalty

20x of QC QC QC QC

Pair XX Catch Catch Catch Pond

PF Unique Orientation Penalty Penalty Picard Penalty Penalty Penalty Pico Pico Pico Pico Reads INS iOOX lOx Data 30x 40X 50X Quant Row Well Column

550 96769505 F 5.49307 4.14 4.25 4.36 4.48428 4.6206 15,28 F F02 2

55 Ϊ 86785560 FR 5.46201 4.11 4.21 4.32 4.44706 4.58119 17, 18 G G02 2

552 108568574 FR 5.34416 4.07 ' 4.17 4.28 4.40Ϊ05 ' 4.52766 17,2 H ' H02 2

553 94644143 FR 5.60546 4,22 4.33 4.45 4.57407 4.7024 15.79 A A03 3

554 123476996 FR 5.7905 4.3 4.23 4.35 4.50497 4.66792 13.38 D D03 3

555 98598372 FR -3 30.5 11.39 12.52 34.04821 16.25787 16.62 _F F03 3

556 118408079 FR 5.76034 4.33 4.43 4.55 4.67059 4.81971 16.13 G G03 3

557 115725927 FR -3 32.49 13.6 15 36.97.648 19.78329 14.82 A A04 4

558 109559233 FR 7.91698 4.9 5.09 5.29 5.51984 5.778 14.95 B B04 4

559 97474352 FR 5.60373 4.3 4.22 4.34 4,47334 4.6173 13.52 C C04 4

560 108693339 FR 5.67259 4.08 4.2 4.33 4,4689 4.62383 14.43 D D04 4

561 82759418 FR 5.8651 4.12 4.25 4.39 4,53143 4.69863 14.57 E E04 4

562 106620097 FR 6.64143 4.59 4.73 4.89 5.06306 5.24647 34.61 F F04 4

563 102996828 FR 5.81063 4.17 4.29 4.42 4.56493 4.7366 35.33 G G04 4

564 101731565 FR 5.74472 3.92 4.05 4.18 4.34007 4.50741 37.67 H II04 4

565 43812835 FR NA 4.88 8.35 -1 NA NA 3 3.97 A A 10 30

566 36954976 FR NA 7.71 -3 -1 NA NA 30.5 B BIO 30

567 147932946 FR NA 4.16 4.34 4.52 NA NA 30,69 C CIO 30

568 92599780 FR NA 4.22 4.73 5.41 NA NA 3 3 ,88 D D10 30

569 1 52808924 FR NA 4.3 4.42 4.55 NA NA 33, 19 £ EI0 30

570 34299484 FR NA 7.18 -1 -1 NA NA 12,32 F F10 1

57Ϊ 131551307 FR NA 4.26 ' 4.35 4.43 NA ' NA 16,79 G ' GIO 1

572 135886097 FR NA_¬ 4.21 4.29 4.38 NA NA 16.92 II HIO 10

573 20938389 FR NA -1 -1 -3 NA NA 7.59 B B3 1 11

574 143934933 FR NA 4.28 4.44 4.62 NA NA 13.03 C C3 1 11

575 54036105 FR NA 5.3 5 7.52 -3 NA NA 11.05 D Di i 11

576 121396832 FR NA 4.55 4.65 4.76 NA NA 16.13 E El 3 11

577 115837547 FR NA 4.37 4.55 4.75 NA NA 12.95 C C32 12

578 126274787 FR NA 4.3 3 4.22 4.34 NA NA 14.34 D DI2 12

579 57159880 FR NA 4.92 6.96 -1 NA NA 11.58 E E12 12

580 191909246 FR NA 4.75 4.87 4.98 NA NA 12.86 G G12 12

581 98373 Π7 FR 5.50417 4.57 4.66 4.74 4,82987 4.93543 12.08 A A01 1

582 126887046 FR NA 4.2 4.28 4.35 NA NA 33.11 C C01 3

583 121853568 FR NA 4.65 4.73 4.82 NA NA 33.5 F F01 3

584 103227938 FR NA 5.18 5.33 5.46 NA NA 3 2.45 G GO! 3

585 1 37488028 FR NA 4.02 4.33 4.7.6 NA NA 30.36 H HO 3 3

586 1 7.6464962 FR NA 4.22 4.28 4.34 NA NA 34.37. A A02 2

587 107415069 FR NA 5.09 5.22 5.36 NA NA 34,84 B B02 2

588 1 0506267 FR NA 4.61 4.74 4.87 NA NA 32,73 C C02 2

589 120240875 FR 4.75666 4.18 4.24 4.29 4.34876 4.4104 14,7 D D02 2

590 103835849 FR NA 4.97 ' 5. Ϊ Ϊ 5.25 NA ' NA 14,37 G ' G02 2

59i 97530548 FR NA_¬ 4.83 5.35 6.05 NA NA 12.36 II H02 2

592 110709971 FR NA 4,45 4.67 4.9 NA NA 14.42 B B03 3

593 130006279 FR NA 4,76 5.07 5.44 NA NA 12.24 C C03 3

594 1498361 58 FR NA 4.49 4.57 4.66 NA NA 13.42 D D03 3

595 118457693 FR NA 4 4.32 4.7 NA NA 11.51 F F03 3

596 105462740 FR NA 5.23 6.03 7.41 NA NA 10.68 G G03 3

597 112469736 FR NA 4.28 4.39 4.49 NA NA 10.26 H H03 3

598 121503399 FR NA 4.53 4.63 4.75 NA NA 12.93 A A04 4

599 143741828 FR NA 4.13 4.28 4.43 NA NA 11.78 B B04 4

600 138074582 FR NA 4.42 4.52 4.64 NA NA ΪΙ.83 C C04 4

601 154800401 FR NA 4.2 4.33 4.49 NA NA 32.44 D D04 4

602 117550726 FR NA 4.2 4.33 4.48 NA NA 32.57 E E04 4

603 145007543 FR NA 4.04 4.19 4.34 NA NA 32.78 F F04 4

604 1 7.4692219 FR NA 4.35 4.49 4.65 NA NA 9.39 H H04 4

605 1 17826928 FR NA 4.18 4.3 4.43 NA NA 3 2.32 A AOS 5

606 1 1264996 FR NA 4.05 4.2 4.37 NA NA 3 3 ,34 B B05 5

607 1 32440272 FR NA 4 4.12 4.23 NA NA 32,84 C C05 5

608 113670741 FR NA 4.01 4.09 4.19 NA NA 11,88 D DOS 5

609 146863159 FR NA 4.15 4.25 4.34 NA NA 12, 15 E EOS 5

610 120210100 FR NA 4.03 ' 4.13 4.24 NA ' NA 13,09 F ' F05 5 Penalty

20x of QC QC QC QC

Pa r XX Catch Catch Catch Pond

PF Unique Orientation Penalty Penalty Picard Penalty Penalty Penalty Pico Pico Pico Pico Reads INS iOOX lOx Data 30x 40X 50X Quant Row Well Column

611 143986974 F NA 4.19 4.29 4.39 NA NA 12,86 H H05 5

612 131045900 FR NA 4.18 4.28 4.39 NA NA 12,77 A A06 6

613 142652263 FR NA 4 ' 4.12 4.27 NA ' NA 11,32 B ' B06 6

614 136763795 FR NA_¬ 4.34 4.32 4.54 NA NA 11.46 C C06 6

615 144200950 FR NA 4.01 4.11 4.23 NA NA 11.11 Ό D06 6

616 18779700 FR NA 5.04 5.23 5.45 NA NA 13.12 _E , E06 6

617 106460139 FR NA 4.38 4.33 4.48 NA NA 12.15 F F06 6

618 107970919 FR NA. 4.33 4.39 4.69 NA NA 11.44 G G06 6

619 139610305 FR NA 4.23 4.36 4.51 NA N 8.58 H H06 6

620 119638682 FR NA 4.32 4.46 4.61 NA N 12.78 A A07 7

621 136625852 FR NA 4.17 4,25 4.33 NA NA 12.1 B B07 7

622 122571998 FR NA 4.3 4,39 4.48 NA NA 12.69 C CO 7 7

623 130372262 FR NA 4.14 4.23 4.29 NA NA 32.82 D D07 7

624 123844483 FR NA 4.15 4.23 4.33 NA NA 3 1.85 E E07 7

625 111052534 FR NA 4.21 4.29 4.38 NA NA 32.03 F F07 7

626 125121039 FR NA 4.21 4.29 4.37 NA NA 33.66 G G07 7

627 102339632 FR NA 4.65 4.74 4.84 NA NA 33.2 A AOS 8

628 134383684 FR NA 4.2 4.29 4.38 NA NA 32,63 B BOS 8

629 1 14855438 FR NA 4.39 4.5 4.62 NA NA 33,18 C COS 8

630 1 5945757 FR NA 4.25 4.32 4.4 NA NA 33,06 D DOS 8

631 140075631 FR NA 4.2 4.28 4.36 NA NA 12,66 E EOS 8

632 137712042 FR NA 4.17 ' 4.24 4.32 NA ' NA 13,59 F ' F08 8

633 135092145 FR NA_¬ 4.22 4.3 4.39 NA NA 14.09 G G08 8

634 108873009 FR NA 4.3 4.37 4.45 NA NA 8.89 II H08 8

635 90015476 FR NA_¬ 4.26 4.35 4.44 NA NA 12.88 A A09 9

636 18186417 FR NA 4.49 4.62 4.77 NA NA 12.59 B B09 9

637 129426372 FR NA. 4.72 4.83 4.93 NA NA 12.75 D D09 9

638 100259649 FR 6.3685 4.45 4.59 4.74 4,9048 5.08805 13.78 E E09 9

639 129206705 FR NA 4.72 4.93 5.18 NA N 13 F F09 9

640 121821209 FR NA 4.16 4.3 4.48 NA NA 11.79 A A10 10

641 89584281 FR NA 4.25 4,83 5.72 NA NA 9.6 B B10 10

642 33999249 FR -Ϊ 6.98 -1 -Ϊ -1 -1 8.8Ϊ C CIO 10

643 125299091 FR NA 4.19 4.33 4.43 NA NA 32.31 D D10 30

644 130569187 FR NA 3.92 4.12 4.35 NA NA 3 1.49 E EiO 30

645 146627455 FR NA 3.97 4.33 4.29 NA NA 3 3.85 F F30 30

646 1 11706332 FR NA 4.05 4.23 4.38 NA NA 32.82 G G10 30

647 1 18400718 FR NA 4.15 4.27 4.39 NA NA 3 3.41 H HtO 30

648 209055969 FR NA 3.88 4.02 4.17 NA NA 30,76 A Al l 3 3

649 103958420 FR NA 4.28 4.52 4.79 NA NA 3 3 ,09 B BI 1 3 3

650 124048726 FR NA 4.13 4.23 4.31 NA NA 12,62 C Cl l 11

651 125367453 FR NA 4.17 ' 4.25 4.34 NA ' NA 13,71 D Dl i 11

652 131193120 FR NA 4.26 4.47 4.71 NA NA 12.55 E El l 11

653 118732523 FR NA 4.22 4.32 4.43 NA NA 13.72 G Gi l 11

654 130653355 FR NA 4.28 4.37 4.45 NA NA 11.77 II Hi ! 11

655 71148837 FR -3 5.68 6.56 7.97 30.90165 -1 23.26 A AO! NA

656 76894289 FR NA. 4.7 5.25 6.04 NA NA 23.02 B B03 NA

657 70629252 FR NA 4.85 5.56 6.7 NA N 27.52 C CO 3 NA

658 83440969 FR NA 4.77 5.35 6.19 NA N 25.1 D DOi NA

659 77528421 FR NA 4.72 5.33 6.25 NA N 22.68 F F01 NA

660 63432640 FR NA 4.87 5.64 6.88 NA NA 24.91 G GOI NA

661 83043834 FR NA 4.92 5.63 6.75 NA NA 22.82 H H01 NA

662 71148895 FR NA 4.9 5.59 6.62 NA NA 26.87 A A02 NA

663 65559974 FR NA 4.98 5.75 7 NA NA 25.87 B B02 NA

664 80038442 FR NA 5.63 6.39 7.56 NA NA 25.18 C C02 NA

665 74246181 FR NA 4.93 5.67 6.8 NA NA 25.22 D D02 NA

666 70151398 FR NA 4.89 5.58 6.65 NA NA 25.81 E E02 NA

667 64817524 FR NA 5.06 5.94 7.49 NA NA 24.62 F F02 NA

668 62518545 FR NA 5.01 5.93 7.61 NA NA 24.23 G G02 NA

669 114331178 FR NA 4.6 5.15 5.93 NA NA 23,13 II H02 NA

670 75882033 FR NA 4.91 5.56 6.55 NA NA 41,67 B B03 NA

671 69846001 FR NA 5.07 ' 6.04 7.81 NA ' NA 25,4 D ' D03 NA Penalty

20x of QC QC QC QC

Pa r XX Catch Catch Catch Pond

PF Unique Orientation Penalty Penalty Picard Penalty Penalty Penalty Pico Pico Pico Pico Reads INS iOOX lOx Data 30x 40X 50X Quant Row Well Column

672 59502794 F NA 6.77 9.34 -i NA NA 24,22 E E03 NA

673 68231958 FR NA 5.09 6.11 8.09 NA NA 22 G G03 NA

674 67260458 FR NA 4.91 ' 5.73 7.1 NA ' NA 21,78 H ' H^"03 NA

675 77450131 FR NA_¬ 4,82 5.41 6.26 NA NA 26 A A04 NA

676 68088616 FR NA 4,9 5.62 6.75 NA NA 32.45 Ft B04 NA

677 52527972 FR -3 5.33 6.45 9.83 -i -I 23.34 _C , C04 NA

678 71991904 FR NA 5.54 6.68 8.96 NA NA 35.31 D D04 NA

679 65679529 FR NA 5.09 6. i t 8.03 NA NA 23.07 E E04 NA

680 68633051 FR NA 4.98 5.77 7.08 NA N 22.08 H H04 NA

68 i 74446094 FR NA 5.02 5.71 6.76 NA N 32.17 B BOS NA

682 71630368 FR NA 5.08 5.97 7.54 NA NA 23.32 C COS NA

683 45197328 FR NA 5.54 7.55 -Ϊ NA NA 23.3 D D05 NA

684 56150917 FR NA 5.24 6.43 9.07 NA NA 24.63 E E05 NA

685 1 11397425 FR 4.88513 4.19 4.25 4.32 4.3854 4.45962 33.02 A A01 3

686 1 44636212 FR 4.78222 4.14 4.2 4.26 4.33109 4.39884 33.01 B B01 3

687 143282090 FR 4.92352 4.3 4.35 4.42 4.48308 4.55059 3 2.93 C CO I 3

688 149456997 FR 5.44971 4.64 4.72 4.79 4.87486 4.95845 3 2.69 D DO 3 3

689 1 36339475 FR 4.897 4.17 4.24 4.31 4.37714 4.463 39 32.38 F FOi 3

690 109186506 FR 5.16819 4.41 4.48 4.55 4.62763 4.70484 3 3 .85 G GO I 3

69 i 143801529 FR 4.98409 4.28 4.34 4.41 4.48378 4.55303 30.78 H HO 1 3

692 129248240 FR 5.0497 4.21 4.28 4.36 4.44692 4.52709 15, 19 A A02 2

693 122048755 FR 5.12084 4.24 ' 4.32 4.39 4.48763 ' 4.57Ϊ68 14,37 B ' B02 2

694 125664781 FR 5.18305 4,3 4.38 4.45 4.54383 4.63775 14.57 C C02 2

695 130165828 FR 4.9365 4,23 4.3 4.36 4.43821 4.51192 14.14 D D02 2

696 138321751 FR 5.0997 4,32 4.39 4.46 4.54294 4.62248 13.72 E E02 2

697 138528306 FR 4.96842 4.3 5 4.22 4.3 4.37493 4.46387 13.76 F F02 2

698 102507031 FR 5.23785 4.39 4.46 4.54 4.63191 4.72042 14.4 G G02 2

699 126072145 FR 4.99934 4.36 4.24 4.32 4,40059 4.49025 12.59 H H02 2

700 1063781 29 FR 5.34265 4.49 4.56 4.65 4,72675 4.8215 15.71 B B03 3

701 86684923 FR NA 5.57 6.23 7.15 NA NA 13.06 A A01 1

702 118476562 FR NA 4.89 5.21 5.58 NA NA 13.5 B B01 1

703 ΙΪ8434090 FR 0 6.31 6.75 7.27 0 0 14.07 C C01 1

704 72971470 FR NA 5.87 8.17 -1 NA NA 32.66 D DO! 3

705 103964480 FR NA 5.09 5.55 6.12 NA NA 34.2 F F01 3

706 78838374 FR N 5.05 6.37 8.53 NA NA 33.38 G GO! 3

707 50885887 FR N -1 -1 -1 NA NA 3 2.76 H HO 3 3

708 77439610 FR N 6.06 9.39 -1 NA NA 34.27 A A02 2

709 91904512 FR NA 5.48 6.63 8.87 NA NA 32.02 B B02 2

710 61 191564 FR NA 5.69 8.76 -1 NA NA 3 3 .13 C C02 2

711 9248029 FR NA -1 -1 -i NA NA 14,09 D D02 2

712 77640346 FR NA 5.46 ' 6.8 9.98 NA ' NA 14,29 E ' E02 2

713 94662439 FR NA_¬ 4,44 4.89 5.5 NA NA 15.13 F F02 2

714 88002154 FR NA 5.39 5.58 6.08 NA NA 16.69 G G02 2

715 108520912 FR NA_¬ 4,95 5.28 5.66 NA NA 14.33 H H02 2

716 92756536 FR NA 4.93 5.31 5.76 NA NA 16.22 B B03 3

717 100406850 FR NA 5.3 2 5.52 6.04 NA NA 16.6 C C03 3

718 92029026 FR NA 5.3 5.71 6.21 NA N 15.54 D D03 3

719 90367695 FR NA 4.86 5.28 5.81 NA N 15.63 E E03 3

720 97013428 FR NA 4.62 5.1 5.73 NA N 14.07 F F03 3

721 101137414 FR NA 4.7 5.06 5.5 NA NA 15.4 G G03 3

722 156946355 FR NA 5.04 5.45 5.96 NA NA 15.29 H •103 3

723 102714553 FR 5.1136 4.33 4.4 4.47 4.55997 4.63971 33.26 A A01 3

724 1 23312724 FR 5.45232 4.44 4.53 4.62 4.72072 4.82483 34.15 B B01 3

725 1 24838292 FR 6.02476 5.06 5.15 5.23 5.33043 5.43359 34.76 C C01 3

726 140752553 FR 7.35175 6.29 6.38 6.49 6.59467 6.69664 3 5.53 D DO 3 3

727 1 22984347 FR 5.1 5705 4.49 4.56 4.62 4.68754 4.76283 34 F FOi 3

728 91 759730 FR 5.1 7551 4.38 4.45 4.53 4.60949 4.69294 3 5 G GO I 3

729 1 26393288 FR 5.2155 4.4 4.47 4.54 4.62539 4.70887 34.26 H HOI 3

730 132588372 FR 6.61526 5.48 5.58 5.69 5.79277 5.91451 16,09 A A02 2

731 119730561 FR 6.82693 5.73 5.82 5.93 6.03436 6.1506 15,25 B B02 2

732 126529228 FR 5.17967 4.28 ' 4.36 4.44 4.53694 ' 4.62792 13,78 c ' C02 2 Penalty

20x of QC QC QC QC

Pa r XX Catch Catch Catch Pond

PF Unique Orientation Penalty Penalty Picard Penalty Penalty Penalty Pico Pico Pico Pico Reads INS iOOX 10x ^" Data 30x 40X 50X Quant Row Well Column

733 12932S039 F 6.55319 5.44 5.54 5.64 5.75662 5.87207 15,48 D D02 2

734 134811357 FR 5.41587 4.63 4.7 4.78 4.86393 4.93752 14,96 E E02 2

735 134435000 FR 21.40863 12.43 * Ϊ2.94 13.51 14.15163 ' Ϊ4.886 14,21 F ' F02 2

736 94734079 FR 5.7709 4.85 4.94 5.02 5.11351 5.20683 15.79 G G02 2

737 113598937 FR 5.08089 4.31 4.38 4.45 4.52608 4.60936 14.53 II H02 2

738 13469691 1 FR 7.4812 6.33 6.25 6.38 6.50603 6.64363 15.7 _B , B03 3

739 131954247 FR 6.08385 5.06 5.15 5.24 5.34844 5.45264 15.4 C C03 3

740 153608233 FR 7.80033 6.42 6.54 6.68 6.80768 6.95291 15.41 D D03 3

74 i 123678681 FR 5.73221 4.7 4.79 4.89 4.98661 5.09597 14.56 E E03 3

742 127586738 FR 5.016 4.24 4.31 4.39 4,46078 4.54845 14.03 F F03 3

743 123265254 FR 5.15507 4.35 4.42 4.5 4,57766 4,66294 13.56 G G03 3

744 105384444 FR 5.01129 4.3 4.36 4.43 4,5042 4,57932 15.07 H H03 3

745 98492892 FR 5.97947 5 5.09 5.18 5.28333 5.37971 36.61 A A0 4

746 1 28521142 FR 5.11973 4.22 4.29 4.38 4.4646 4.55605 34.05 B B04 4

747 1 17149949 FR 5.43804 4.45 4.53 4.62 4.72165 4.8251 4 34.35 C C04 4

748 1 36549732 FR 6.31213 5.31 5.39 5.49 5.5879 5.69336 3 5.03 D D04 4

749 1 25586959 FR 6.92597 5.76 5.87 5.98 6.08877 6.23037 34.06 E E04 4

750 1 5187849 FR 5.87696 4.99 5.07 5.15 5.23804 5.3303 1 34,3 F F04 4

75 i 98841198 FR 5.23427 4.46 4.53 4.6 4.68804 4.76044 3 5,63 H H04 4

752 1 10969566 FR 5.62873 4.52 4.63 4.71 4.82023 4.9292 36,59 A AOS 5

753 99606577 FR 5.7234S 4.68 4.77 4.87 4.97262 5.0818 15,77 P. BOS 5

754 117280115 FR 6.24071 4.92 ' 5.03 5.14 5.27755 ' 5.41058 14,94 c ' COS 5

755 86730626 FR 5.20228 4.27 4.35 4. 4 4.53193 4.62272 12.46 D DOS

756 118851028 FR 5.14673 4.2 4.28 4.37 4.459 4.5549 12.36 E E05

757 110163911 FR 6.543 5.49 5.58 5.68 5.78683 5.88797 13.7 F F05

758 124426874 FR 5.52399 4.62 4.7 4.79 4.86972 4.97124 13.96 G G05 5

759 110946832 FR 5.53248 4.67 4.75 4.83 4.9182 5.01053 14.75 H H05 5

760 110446079 FR 5.33754 4.35 4.44 4.53 4,62545 4.73043 14.58 A A06 6

76 i 110783877 FR 5.1866 4.21 4.3 4.39 4,47995 4.58454 14.23 B B06 6

762 119698394 FR 5.21828 4.18 4.26 4.35 4,45999 4.56792 12.52 C C06 6

763 129029461 FR 6.53512 5.42 5.53 5.63 5,74097 5.85606 14.49 D D06 6

764 156749500 FR 6.3746 5.15 5.26 5.37 5,47987 5.60896 Ϊ4.6Ϊ E E06 6

765 97910326 FR 5.02268 4.23 4.3 4.38 4.45747 4.54258 33.7 F F06 6

766 89971519 FR 5.57366 4.49 4.58 4.68 4.77873 4.88829 33.18 G G06 6

767 1 14006239 FR 5.21916 4.25 4.34 4.42 4.52329 4.62045 34.94 H H06 6

768 1 16996272 FR 5.3268 4.3 4.39 4.48 4.57662 4.6865 34.79 A A07 7

769 1 1 8484617 FR 5.25009 4.22 4.33 4.4 4.49588 4.6068 34.44 B B07 7

770 1 1 2286738 FR 5.30581 4.27 4.35 4.45 4.5489 4.65346 32,78 C C07 7

77 i 1 091267 Ϊ FR 5.29025 4.35 4.43 4.52 4.60657 4.70662 32,6 D D07 7

772 112560768 FR 5.04706 4.27 4.35 4.42 4.49576 4.57852 12,76 E E07 7

773 108389906 FR 6.2354 5. is *^" 5.27 5.37 5.47785 ' 5.58333 13,69 F ' F07 7

774 120683448 FR 6.02343 4.89 4.99 5.09 5.20066 5.31128 12.91 G G07 7

775 103045906 FR 5.05334 4.37 4.44 4.5 4.56706 4.64112 14.87 II H07 7

776 98964880 FR 5.20024 4.28 4.36 4. 4 4.53275 4.63065 14.84 A AOS 8

777 120328432 FR 5.24736 4.27 4.35 4.45 4.5356 4.63329 13.05 B BOS 8

778 127814222 FR 8.20547 6.5 6.64 6.79 6.95518 7.13056 14.01 C COS 8

779 115271740 FR 5.54877 4.45 4.54 4.64 4,74867 4.85765 11.49 D DOS 8

780 117890607 FR 5.18866 4.31 4.39 4.47 4.55153 4.651 12.83 E EOS 8

78 i 134394760 FR 6.54758 5.64 5.72 5.82 5.90162 6.00486 13.53 F F08 8

782 126093496 FR 7.01512 5.86 5.96 6.08 6,18147 6.30611 13.79 G G08 8

783 Ϊ01189576 FR 6.Ϊ2632 5.05 5.14 5.24 5,3552 5.46663 Ϊ4.9Ϊ H H08 8

784 84319117 FR 5.52048 4.34 4.45 4.55 4.6551 4.7798 33.3 A A09 9

785 98649137 FR 5.32464 4.35 4.44 4.53 4.62572 4.723 33 34.82 B B09 9

786 1 16689872 FR 5.18617 4.28 4.36 4.45 4.53938 4.62795 33.82 D D09 9

787 1 13409335 FR 5.20368 4.3 4.38 4.47 4.55162 4.64477 3 2.55 E E09 9

788 108399988 FR 5.73462 4.45 4.55 4.67 4.78187 4.93581 33.43 F F09 9

789 108962100 FR 6.0892 4.98 5.07 5.17 5.27987 5.39333 34,52 G G09 9

790 1 10085526 FR 5.1 5856 4.27 4.34 4.42 4.51757 4.60555 33.49 H H09 9

79 Ϊ 96526S93 FR 5.36486 4.28 4.37 4.47 4.57276 4.67837 16,04 A A10 10

792 117337368 FR 5.59757 4.25 4.35 4.47 4.59028 4.72216 13,58 B B10 10

793 94963531 FR 5.42378 4.46 ' 4.55 4.63 4.7269 ί ' 4.8307 13.11 c ' cio 10

Penalty

20x of QC QC QC QC

Pair XX Catch Catch Catch Pond

PF Unique Orientation Penalty Penalty Picard Penalty Penalty Penalty Pico Pico Pico Pico Reads INS iOOX 10x ^" Data 30x 40X 50X Quant Row Well Column

855 107796187 F NA 7.12 8.71 12.14 NA NA 14,32 B B06 6

856 118160399 FR NA 7.34 8.61 10.8 NA NA 15,54 C C06 6

857 112441046 FR -1 10.83 ' 16,68 -1 -i ' -i 15,6 D ' D06 6

858 110499489 FR -3 8.06 9.32 11.42 36.03665 -1 17.12 E E06 6

859 119998366 FR NA 6.23 7 8.08 NA NA 14.81 G G06 6

860 149048894 FR NA 4.36 4.45 4.55 NA NA 15.5 _H , H06 6

86i 33258469 FR NA -1 -1 -3 NA NA 7.47 A A07 7

862 161339265 FR NA. 8.26 9.21 10.49 NA NA 14.02 B B07 7

863 142074609 FR NA 4.58 4.69 4.8 NA N 14.36 A A02 1

864 130261407 FR NA 4.32 4.42 4.54 NA N 16.3 B B02 1

865 142756968 FR NA 4.44 4.56 4.7 NA NA 15.4 C C02 1

866 143129468 FR NA 4.34 4.44 4.54 NA NA 16.26 D D02 1

867 101223416 FR NA 4.67 4.82 4.99 NA NA 33.96 E E02 3

Ref non

OXO

Bases Target Total Bases Total PF Total Reads Total Reads Total Reads OXO External ID Territory OXO Bases AP Al HS

788 40494560 E7120080-15 32950014 81197182 9385773368 130874280 330874280 130874280

789 38134439 AA301442-36 32950014 76449773 9049401928 126286996 326286996 126286996

790 42316867 AA777349-36 32950014 84821134 9322607944 129698910 329698910 129698910

79 i 36690157 AA080288-36 32950014 73527721 8170614688 113925624 3 33925624 113925624

792 44493099 AA070821-36 32950014 89170768 10459238864 145356102 145356102 145356102

793 36032486 E7269629-15 32950014 72255776 7896937168 I ! 0077286 1 30077286 110077286

794 39030415 AA589261-16 32950014 78253321 9126065712 127185584 127185584 127185584

793 ' 138371^" Α07 5 Ϊ-Ϊ6 32950014 277981 3793514312 ' 53359Ϊ34 53359134 53359134

796 623585 ΑΑ508592-Ϊ6 32950034 3254024 6055662672 85254178 85254378 85254178

797 60726 ΑΑ872286-Ϊ6 32950034 322036 4715226200 67349286 67349286 67349286

798 179719 E7697463-15 32950034 362029 6079049392 85433234 85433234 85433234

799 99840 E7003155-J 5 32950034 399814 7508125120 108525732 108525732 108525732

800 239386 AB600516-16 32950034 480264 6158173752 88093924 88093924 88093924

80! 47591712 0100056 N 32950014 95432523 11902320480 164796026 164796026 164796026

802 45943109 0200023 N 32950014 92044466 11064441760 153241434 153241434 153241434

803 67818481 0200038 T 32950014 134392006 17453076696 242898842 242898842 242898842

804 35922240 0200016 N 32950014 72017740 8813620592 122061000 122061000 122061000

805 1336766 Sr¾5-17068T 32956014 2689969 ' Ϊ4758465536 206623648 206623648 ' 206623648

806 1026105 SP05 -^"l7()68N 32950014 2062082 ' Ϊ2394806732 173637956 373637956 173637956

807 40310536 0200038 N 32950014 80768680 ' 9890600024 136856076 336856076 136856076

808 14988466 H03-48252T 32950014 29497824 15198346392 213331650 213131650 213131650

809 6227885 H03-48252N 32950014 12288239 14483598920 202351052 202151052 202151052

810 39423703 0100056 T 32950014 78479663 10674176288 147775250 347775250 147775250

811 39643547 0200023 T 32950014 78697077 10357003512 143190102 143190102 143190102

812 42249750 0200016 T 32950014 83866! 54 11147242088 154328964 154328964 154328964

813 32008778 0200036 T 32950014 63638350 8549364944 118368872 118368872 118368872

814 5417224 H03-4693T 32950014 10779242 13289422472 185262872 185262872 185262872

815 ' 48241906 0200036 N 32950014 96713597 12167744248 ' Ϊ69069Ϊ 14 169069114 169069114

816 4217490 ΪΪ03 -4693Ν 32950034 8410603 12992790976 183685772 183685772 183685772

817 1055262 SP05-5957N 32950034 2116033 10499744584 146201636 146203636 146201636

JLLL 49789907 AB746668-16 32950034 99844403 13789428144 196403012 196403012 196403012

819 57222559 AB606529-26-2 32950034 3 33822770 15326436336 218026800 218026800 218026800

820 43296178 AB603460-16 32950034 86800780 12098391816 170870804 170870804 170870804

821 59168241 AA329088-5-2 32950014 1 37676780 15457911168 219378320 219378320 219378320

822 54353202 Pat.44.BRAF2 32950014 107871399 16383647848 232230706 232230706 232230706

823 39568334 Pat 42.BRAF2 32950014 78642898 9219438248 130461960 130461960 130461960

824 54839505 Pat 3 .BRAF2 32956014 108817750 ' Ϊ4376394992 203042292 203042292 ' 203042292

825 40513549 DFCi.ii -^"l04.i4 alicuot 2 32950014 81179329 ' Ϊ1683858480 165546610 365546610 165546610

826 50025707 AA2₅0770-36 32950014 100289798 ' 13895229568 195527490 395527490 195527490

827 44090234 ΛΒ609648-16 32950014 88401636 11512964120 162714126 362714126 162714126

828 49666498 Pat I9.BRAF2 32950014 98361335 14042503432 199323396 399123396 199123396

829 46642201 AA376502-36 32950014 93541834 12541870664 177550288 377550288 177550288

830 50027842 AA 76916-23 32950014 100334463 12412357696 176035170 176015170 176015170

831 42839496 AA863715-16 32950014 85885716 10491677792 147642476 147642476 147642476

832 59707924 AA383940-54-3 32950014 1184! 4296 13270902792 187433138 187413138 187413138

833 53600121 Pat 26.BRAF2 32950014 105936749 15450923576 219401246 219401246 219401246

834 ' 46709449 Pat ΪΪ.Β Ϊ'2 32950014 93207322 13446236008 ' Ϊ912 1180 191241180 191241180

835 50751272 Pat 04.B3lAF2 32950034 300698173 Ϊ539Ϊ8Ϊί232 218270036 218270036 218270036

836 60304559 AA863712-26-3 32950034 3 19585246 14030703056 198083832 198083832 198083832

837 47613654 AB728427-19 32950034 95489918 10927739800 154313758 154313758 154313758

838 52997271 Pat 37.BRAF2 32950034 305209989 14687867008 208782814 208782814 208782814

839 45056548 AA863718-I6 32950034 90426415 10220059720 144710650 144710650 144730650

840 41721965 AA447688-26-2 32950014 83013398 I ! 836878248 167213244 1672! 3244 167233244

84! 52354109 Pat 14.BRAF2 32950014 103813770 14343921256 202963796 202963796 202963796

842 45091225 BOT2745-6T tumor 32950014 90387722 11284196520 159530170 159530170 159530170

843 45265764 BOT2868-2T tumor 32950014 90768628 12195449136 173357362 173357362 173357362

844 28343725 EL12-S3X xenograft 32950014 56808366 * 8528277224 120599410 120599410 ' Ϊ20599410

845 45289764 BOT2935-2T tumor 32950014 90793642 ' 11553271480 163445074 363445074 163445074

846 39197074 E12-19X xenograft 32950014 78651138 8606222520 123639054 321639054 121639054

847 39681918 BOTELl 1 -26X xenograft 32950014 79513004 10416691328 147830016 347830016 147830016

848 64953365 AB765990-26-2 32950014 128873882 11814839008 167901524 367901524 167901524

849 46304657 BOT2745-1 ON normal 32950014 92814968 12318394336 175053102 375053102 175053102

[00260] Supplementary Table 2. Turnaround time for a cohort of FFPE samples. For 28 demonstrative FFPE cases, turnaround time in days is provided in this table. The time to exome data delivery was 17.4 ± 2.2 days (median ± s.d; 25th/75th percentiles 14.3 and 18.6) for FFPE samples received as DNA and 20.1 ± 2.4 days (median ± s.d; 25th/75th percentiles 17.5 and 21.2) days for samples received as FFPE tissue blocks. Turnaround

time (days):

receipt

FFPE t

Sample aggregation Workflow

1 17.52 Extraction, sample prep, and sequencing (received as tissue)

2 17.52 Extraction, sample prep, and sequencing (received as tissue)

3 18.9 Extraction, sample prep, and sequencing (received as tissue)

4 14.18 Sample prep and sequencing (received as DNA)

5 14.28 Sample prep and sequencing (received as DNA)

6 14.28 Sample prep and sequencing (received as DNA)

14.22 Sample prep and sequencing (received as DNA)8

14.32 Sample prep and sequencing (received as DNA)

9 18.53 Sample prep and sequencing (received as DNA)

10 1 8.69 Sample prep and sequencing (received as DNA)

1 1 1 8.74 Sample prep and sequencing (received as DNA)

12 17.07 Sample prep and sequencing (received as DNA)

3 18.42 Sample prep and sequencing (received as DNA)

14 18.61 Sample prep and sequencing (received as DNA)

15 18.88 Sample prep and sequencmg (received as DNA)

16 22.01 Extraction, sample prep, and sequencing (received as tissue)

17 15.3 Extraction, sample prep, and sequencing (received as tissue)

18 15.72 Extraction, sample prep, and sequencing (received as tissue)

19 15.72 Extraction, sample prep, and sequencing (received as tissue)

20 19.04 Extraction, sample prep, and sequencing (received as tissue)

21 20.81 Extraction, sample prep, and sequencing (received as tissue)

22 20.89 Extraction, sample prep, and sequencing (received as tissue)

23 20.97 Extraction, sample prep, and sequencing (received as tissue)

24 20.81 Extraction, sample prep, and sequencmg (received as tissue)

25 20.89 Extraction, sample prep, and sequencing (received as tissue)

26 22,03 Extraction, sample prep, and sequencing (received as tissue)

27 22,03 Extraction, sample prep, and sequencing (received as tissue)

28 22.03 Extraction, sample prep, and sequencing (received as tissue)

[0Θ261] Supplementary Table 3. Age of FFPE blocks. The age (in years) of the FFPE blocks used for the FFPE and frozen cross-val dation study is provided in this table.

Year of FFPE

Case Block

El 0278 2009

EG1317 2009

[00262] Supplementary Ί e 4. Cross-va idation data for ^'.

sequencing cases. This table includes the number of validated, false positive, and insufficiently powered mutations for FFPE and frozen samples from the same patient at both the original and downsampled (to 90X) coverage values. Additionally, the validation percentage is provided per sample and per cohort.

Regsdar Downsaunpied

Power Power Power Power

ed and ed aisd Instifiice Percen ed and ed arid insiiftice Percen validat fa!se nti t validat false ntiy t ed positiv powered va!idat ed positiv powered vaiidat

Pair ID siies e sites sites ed sites e sites sites ed

Froze LUAD £00565- 589 123 138 0.827 578 113 124 0.836 Tumor

LUAD_E00623- 682 49 187 0.933 645 46 166 0.933 Tumor

LUAD E00905- 62 21 0.747 61 20 38 0.753 Tumor

LUAD E00934- 570 94 0.963 569 22. 87 0.963 Tumor

IUAI> E01047- 228 1 90 0.996 240 3 1 54 0.988 Tumor

LUAD E01086- 94 0 36 1.000 88 1 25 0,989 Turrior

LUAD £01 147- 196 25 67 0.887 193 22 71 0.898 Tumor

LU AD £01 166- 126 6 41 0.955 126 4 29 0.969 Tumor

LUAD_E01217- 495 32 63 0.939 485 30 52 0.942 Tumor

LUAD E01278- 208 1 2 58 0.945 207 8 47 0.963 Tumor

IUAI> E01317- 149 45 51 0.768 148 42 40 0.779 Tumor

Total 3399 336 846 0.910 3340 311 833 0.955

Median 208 22 63 0.939 207 22 52 0.942

Mean 309.00 30.55 76.95 0.91 303.64 28.27 75.73 0.91

FFPE FFPE LU AD £00 452 37 5 i i 0.924 441 20 299 0.957 565 -Tumor

FFPE_LUAD_E00 379 4 634 0.990 322 3 336 0.991 623-Tumor

FFPE LUAD E00 61 16 64 0.792 60 14 34 0,811 905-Tumor

FFPE LUAD E00 558 19 235 0.967 552 13 152 0,977 934-Tumor

FFPF._LUAD_E0 i 354 52 285 0.872 336 50 232 0.870 047-Tumor

FFPE LUAD E01 124 11 127 0.919 123 9 62 0.932 086-Turaor

FFPE LU AD £01 1 70 59 246 0.742 165 53 1 14 0.757 147 -Tumor

FFPE LUAD £01 140 1 5 55 0.903 137 14 35 0.907 166-Tumor

FFPE LUAD E01 445 35 141 0.927 441 32 1 14 0.932 Regular nownsampled

Power Power Power Power

ed and ed and insuffice Percen ed and ed and Inssjfiiee Percen va!idat fa!se iitiy t va!idat fa!se ntiy t ed positiv powered validat ed positiv powered vaiidat pe Pair ID sites e sites sites ed sites e sites sites ed

217 -Tumor

FFPE _LU AD EOi J 03 0 162 S .000 98 0 J 33 1.000

278-Tumor

FFPE __LUAD EOI 137 23 144 0.856 136 17 89 0,889

3 ί 7-Tumor

Total 2923 271 2604 0.915 2811 225 1600 0.926

Median 170 15* 162 0.919 165 14 114 0.932

Meass 265.73 24.64 236,73 0.90 255.55 20.45 145.45 0.91

[0Θ263] Supplementary Table 5. The TARGET Database. By utilizing primary literature, manual curation, and expert opinion, Applicants generated a database of tumor alterations relevant for genomics-driven therapy (TARGET). This database lists genes that may have therapeutic, prognostic, and diagnostic implications for cancer patients. It includes rationales behind each gene, the types of recurrent alterations that have clinical relevance in these genes, and the potential therapies that are linked to alterations in these genes.

Gene Rationale Types of recurrent Examples of alterations Therapeutic Agents

ABL1 Translocations predict sensitivity to R earrangement; imatinib, Dasatinib, tyrosine kinase inhibitors such as Mutation Nilotinib, ABL1 imatinib, dasatinib, and nilotinib. inhibitors Secondary mutations can cause

resistance to these agents.

AKT1 Mutations may predict sensitivity to Mutation AKT/MTOR inhibitors

AKT/MTO inhibitors

AK.T2 Mutations may predict sensitivity to Mutation; Amplification AKT/MTOR inhibitors

AKT/MTOR inhibitors

AKT3 Mutations may predict sensit vity to Rearrangement; AKT/MTOR inhibitors

AKT/MTOR inhibitors Mutation

ALK Translocations predict sensitivity to Rearrangement; Criz tinib, ALK

ALK-inhibitors such as crizotinib. Mutation; Amplification inhibitors Secondary mutations can cause

resistance. Amplification and

activating mutations may also be

sensitive to these agents.

APC Bialielic inactivation may predict Bialielic Inactivation WNT inhibitors

sensitivity to inhibitors of WNT

signaling or anti-TRATL antibodies.

May signal the presence of a

eermline mutation. Gene Rationale Types of recurrent Examples of alterations Therapeutic Agents

AR Amplification may predict resistance Amplification Androgen Deprivation to androgen deprivation in prostate Enzalutamide cancer and may predict sensitivity to

second generation androgen

deprivation or direct androgen

inhibitors

ARAF Activating mutations may predict Mutation Sorafenib,

sensitivity to sorafenib or other RAF Vemurafenib, inhibitors Dabrafenib, RAF inhibitors

ASXL1 Prognostic in myeiodysplastic Mutations

syndromes (MDS)

ATM Biallelic inactivation may predict Biallelic Inactivation PARP Inhibitors sensitivity to PARP inhibitors

ATR Biallelic inactivation may predict Biallelic Inactivation PARP Inhibitors sensitivity to PARP inhibitors

AURKA Amplifications are prognostic in Amplification AURKA Inhibitors colon cancer. It is also the target of

AURKA inhibitors

BAP1 Biallelic inactivation may predict Biallelic inactivation FID AC Inhibitors sensitivity to HDAC inhibitors. May

signal the presence of a germline

mutation.

BCI ? Translocation is Rearrangement BCL2 inhibitors prognostic/diagnostic in some

hematologic cancers and activating

alterations may be sensitive to BCL2

inhibitors

BRAF Mutations predict sensitivity to RAF Mutation; Vemurafenib,

inhibitors. Amplification may predict Amplification; Dabrafenib, RAF resistance to MEK inhibitors. Rearrangement inhibitors MEK

inhibitors

BRCA1 Biallelic inactivation predict Biallelic Inactivation PARP Inhibitor

sensitivity to PARP inhibitors. May

signal the presence of a germline

mutation.

BRCA2 Biallelic inactivation predict Biallelic Inactivation PARP Inhibitor

sensitivity to PARP inhibitors. May

signal the presence of a germline

mutation.

BRD2 Alterations may preict sensitivity to Rearrangement HDAC Inhibitors

HDAC inhibitors, bromodomain Bromodomain inhibitors inhibitors

BRD3 Alterations may preict sensitivity to Rearrangement HDAC Inhibitors

HDAC inhibitors, bromodomain Bromodomain inhibitors inhibitors Gene Rationale Types of recurrent Examples of alterations Therapeutic Agents

BRD4 Alterations may preict sensitivity to Rearrangement HDAC Inhibitors

HDAC inhibitors, bromodomain Bromodomain inhibitors inhibitors cl5orf55 Sensitivity to HDAC inhibitors, Rearrangement HDAC Inhibitors bromodomain inhibitors Bromodomain

inhibitors

CCND1 Amplification may predict resistance Amplification; Hormone therapy to hormone therapy in breast cancer. Rearrangement CDK4/6 inhibitors Amplification may be prognostic in

breast cancer. Amplification may

predict sensitivity to CDK4/6

inhibitors. Translocations are

diagnostic/prognostic in some

hematologic cancers.

CCND2 Amplification may predict sensitivity Amplification; CDK4/6 inhibitors to CDK4/6 inhibitors. Rearrangement

CCND3 Amplification may predict sensitivity Amplification; CDK4/6 inhibitors to CDK4/6 inhibitors. Rearrangement

CCXk i Amplification may predict sensitivity Amplification CKD2 inhibitor

to CDK2 inhibitors.

CDH1 Diagnostic in lobular breast Mutation

carcinoma. In gastric cancer, may

signal the presence of a germline

mutation.

CDK4 Amplification may predict sensitivity Amplification; Mutation CDK 4 6 inhibitors to CDK4/6 inhibitors.

CDK6 Amplification may predict sensitivity Amplification; CDK4/6 inhibitors to CDK4/6 inhibitors. Rearrangement

CDKN1A Deletion may predict sensitivty to Biallelic Inactivation CDK inhibitors

CDK inhibitors

CDKN1 B Deletion may predict sensitivty to Biallelic Inactivation CDK inhibitors

CDK inhibitors

CDKN2A Biallelic inactivation may predict Biallelic Inactivation CDK4/6 inhibitors sensitivity to CDK4/6 inhibitors.

CDKN2B Biallelic inactivation may predict Biallelic Inactivation CDK4/6 inhibitors sensitivity to CDK4/6 inhibitors.

CEBPA Biallelic inactiavtion is an indication Biallelic Inactivation Transplant

for transplant in AML.

CREBBP Biallelic inactivation is Prognostic / Biallelic Inactivation

Diagnostic in leukemia

CRKL Amplification may result in Amplification Gefitinib, Erlotimb, resistance to EGFR inhibition and EGFR inhibitors RAF inhibition. Amplification may Vemurafenib, predict sensitivity to SRC inhibitors. Dabrafenib, RAF inhibitors Dasatinib, SRC inhibitors Gene Rationale Types of recurrent j Examples of alterations j Therapeutic Agents

CTNNB 1 Some prognostic effects in colon Mutations j WNT inhibitors

cancer and gastric cancer. Activation

may mediate resistance to EGFR

TKJs, PI3K inhibitors, and AKT

inhibitors. Activation may predict

sensitivity to inhibitors of WNT

signaling

DDR2 Mutations may predict sensit vity to Mutations j Dasatinib

dasatinib

DNMT.3A May predict sensitivity to DNA Mutations j DNAMT inhibitors methylransferace inhibitors. May be

prognostic in leukemia.

EGFR Mutations targetabie with TKls (both Mutation; j Erlotinib, Gefitinib,

FDA approved and novel). Other Amplification; j EGFR. inhibitors mutations predict resistance to TKIs. Rearrangement

Amplification associated with

response to anii-EGFR Abs in colon

cancer. Amplification also associated

with resistance to ^'IKJs in some

cancers. Rearangement is prognostic

in GBM, HNSCC

EPHA3 Alterations may predict sensitivity to Mutation; Amplification j Dasatinib Ephrin dasatinib or novel ephrin inhibitors. j inhibitors Alterations may be prognostic in

lung cancer

EPHA5 Alterations may predict sensitivity to Mutation; j Dasatinib Ephrin dasatinib or novel ephrin inhibitors Rearrangement 1 inhibitors

ERBB2 Amplifications and mutations predict Amplification; j Trastuzumab,

sensitivity to a.nti-Her2 therapy. Mutations j Lapatinib, TDM1, j Pertuzumab

ERBB3 Alterations may be sensitive to Mutations j Pertuzumab

pertuzumab or novel HER3

inhibitors

ERBB4 Mutations may predict sensitivity to Mutation j Lapatinib

Lapatinib and other anti-EGF family

inhibitors

ERG Fusion with TMPRSS2 shown to Rearrangement j PARP Inhibitor

potentiate sensitivity to PARP

inhibitors

ESR1 Amplification may predict ER Amplification; j Hormonal therapy positivity in breast cancer. Mutation Mutations

may predict resistance to endocrine

therapy in breast cancer.

ETV1 Diagnostic in prostate cancer Rearrangement j

ETV4 Diagnostic in prostate cancer Rearrangement j

ETV5 Diagnostic in prostate cancer Rearrangement j

ETV6 Diagnostic in prostate cancer Rearrangement j Gene Rationale Types of recurrent Examples of alterations Therapeutic Agents

EWSR1 Diagnostic in Ewing sarcoma. Rearrangement

EZH2 Negative prognostic factor in MDS. Mutations EZH2 inhibitors

May predict sensitivity to EZH2

inhibitors

FBXW7 Mutation or loss may predict Biallelic Inactivation MTOR inhibitors sensitivity to MTOR inhibitors. Tubulins Mutations or loss may predict

resistance to anii-tubulm

chemotherapy

FGFR1 Amplification may predict resistance Amplification FGFR Inhibitors to hormonal therapy in breast cancer.

Amplification may predict sensitivity

to FGFR inhibitors

FGFR2 Alterations may predict sensitivity to Mutations; FGFR Inhibitors

FGFR inhibitors Rearrangement

FGFR3 Alterations may predict sensitivity to Mutations; FGFR Inhibitors

FGFR inhibitors Rearrangeme t

FLT3 Mutations predict sensitivity to FLT3 Mutation Sunitinib, FLT3

inhibitors, sunitinib. Secondary inhibitors mutations predict resistance.

GNA11 Mutations may predict sensitivity to Mutation MAPK pathway

MAPK pathway inhibitors inhibitors

GNAQ Mutations may predict sensitivity to Mutation MAPK pathway

MAPK pathway inhibitors inhibitors

GNAS Mutations may be diagnostic of Mutation JAK inhibitors

tumors arising in McCune -Albright

syndrome, and may be targetable

with JAK inhibitors

HRAS Mutations may predict sensitivity to Mutation MAPK pathway

MAPK pathway inhibitors. inhibitors Mutations may predict resistance to

TKJs.

IDFH Prognostic in GBM. Mutations may Mutation IDH inhibitorss

predict sensit vity to TDH inhibitors

IDH2 Prognostic in GBM. Mutations may Mutation IDH inhibitorss

predict sensitivity to IDF! inhibitors

IGF1R Amplification may predict senitivity Amplification IFG1-R Inhibitor to IGFR1-R inhibitors

JAK2 Mutations may predict sensitivity to Mutation ruxolitinib, JAK

JAK2 inhibitors inhibitors

JAK3 Mutations may predict sensitivity to Mutation tofacitinib, J AK

JAK3 inhibitors inhibitors

KDR Activating mutations may predict Mutations KDR. inhibitors

sensitivity to specific inhibitors Gene Rationale Types of recurrent Examples of alterations Therapeutic Agents

KIT Mutations targetable with TKIs (both Mutation; Amplification Imatinib, Sunitinib

FDA approved and novel). Novel KIT Inhibitors Secondary mutations predict

resistance to TKIs. Amplification

also associated with resistance to

TKIs.

KRAS Mutations may predict resistance to Mutation Cetuximab

anti-EGFR therapies (cetuximab, ant- EGFR TKIs). Mutations may predict

sensitivity to MEK inhibitors.

Mutations may be directly targetable

by some therapies (immunotherapies,

viruses). Prognostic in some cancer

types.

MEK

inhibitors

MAP2K1 Mutations predict resistance to RAF- Mutation Vemurafenib, MEK a d MEK- inhibitor inhibitors

MAP2K2 Activating mutations may predict Mutations MEK inhibitors

sensitivty to MEK2 inhibitors

MAP2K4 Possibly prognostic in breast cancer Mutations

MCL1 Amplification may predict resistance Amplification Tubulins

to anti-tubulin chemotherapy

MDM2 Amplification may predict sensitivity Amplification Xul!in. MDM2

to Nutlins and MDM2 inhibitors inhibitors

MDM4 Amplification may predict sensitivity Amplification MDM4 inhibitors to Nutlins and MDM4 inhibitors

MEN I May be prognostic / diagnostic in Bialfelic Inactivation

some cancer types. May signal the

presence of a germline mutation.

MET Amplification may cause resistance Amplification Gefitinib, Erlotinib, to anti-EGFR TKIs. Amplification EGFR inhibitors may predict sensitivity to MET- Crizotinib, MET inhibitors inhibitors

MITF Alterations may be involved in Mutation Vemurafenib,

resistance to RAF inhibition in Dabrafenib, RAF melanoma. May signal the presence inhibitors of a germline mutation.

MLH1 Prognostic / Diagnostic in colon Bialielic Inactivation

cancer

MLL Translocations are prognostic / Rearrangement HD AC Inhibitors diagnostic in some hematologic

malignancies. Alterations may be

sensitive to HDAC inhibitors or

novel inhibitors in development

MPL Mutation may predict sensitivity to Mutation Ruxolitmib, JAK2

JAK2 inhibitors inhibitors Gene Rationale Types of recurrent Examples of alterations Therapeutic Agents

MSH2 Prognostic / Diagnostic in colon Biallelic Inactivation

cancer

MSH6 Prognostic / Diagnostic in colon Biallelic Inactivation

cancer

MTOR Activating mutations may predict Mutation Everolimus,

sensitivity to MTOR inhibitors. Temsirolimus, MTOR Secondary mutations may predict inhibitors resistance to MTOR inhibitors

MYC May be prognostic / diagnostic in Amplification;

some cancer types Rearrangement

NF1 Biallelic inactivation may predict Biallelic Inactivation PI3KVAK1 ^'MTOR sensitivity to PI3K pathway inhibitors inhibitors (PDK/AKT/MTOR). RAF inhibitors

Biallelic inactivation mapy predict MEK inhibitors resistance to RAF and MEK

inhibitors.

NF2 Biallelic inactivation may predict Biallelic Inactivation P13K7AKT/MTOR sensitivity to P13K pathway inhibitors inhibitors (PI3K/AKT/MTOR)

NFKBTA Deletion is prognostic in GBM Deletions

NKX2-1 Diagnostic in lung cancer Amplification

NOTCH 1 Activating mutations and Mutation; Notch Inhibitors

rearrangements may predict Rearrangement

sensitivity to Notch inhibitors

NOTCH 2 Activating mutations may predict Mutation Notch Inhibitors

sensitivity to Notch inhibitors

NPM1 Mutations are an indication for Mutations; Transplant

transplant in AML Rearrangement

NRAS Mutations predict resistance to RAF- Mutation Vemurafenib,

inbibitors. Mutations may be Dabrafenib, RAF sensitive to MEK inhibitors. inhibitors

MEK inhibitors

^'NTRK3 Fusion with ETS factors (in secretory Rearrangement PI3K/AK1 ^'MTOR breast cancer, for example) may inhibitors predict sensitivity to PI3K pathway Dasatinib. src inhibitors inhibitors, SRC inhibitors, and/or IGF1-R inhibitors IGF1 -R inhibitors

PDGFRA Alterations may predict sensitivity to Mutation; Imatininb

imatinib and other TKIs Rearrangeme t

PDGFRB Alterations may predict sensitivity to Rearrangement Imatininb

imatinib and other TKIs Gene Rationale Types of recurrent Examples of alterations Therapeutic Agents

PIK3CA Mutations may predict sensitivity to Mutations PI3K/AKT MTOR

PI3K pathway inhibitors - PI3K inhibitors inhibitors, AKT inhibitors, and

MTOR inhibitors. Mutations may

predict resistance to anti-RTK

therapy, including cetuximab, anti- EGFR TKIs, and trastuzumab and

lapatimb

PIK3R1 Mutations may predict sensitivity to Mutations PI3K/AKT MTOR

PI3K pathway inhibitors^■■■■ PI3K inhibitors inhibitors, AKT inhibitors, and

MTOR inhibitors.

PTCH1 Mutations may predict sensitivity to Mutations Vismodegib, hedgehog hedgehog inhibitors inhibitors

PTEN BiaUeiic inactivation may predict BiaUeiic Inactivation PI3K/AKT MTOR sensitivity to PI3K path way inhibitors inhibitors— PI3K inhibitors, AKT PARP inhimtors inhibitors, and MTOR inhibitors.

BiaUeiic inactivation may predict

resistance to anti-RTK therapy,

including cetuximab, anti-EGFR

TKIs, and trastuzumab and lapatimb.

BiaUeiic inactivation may predict

sensitivity to PARP inhibitors

RAF1 Alterations may predict sensitivity to Mutation; Sorafenib

RAF inhibitors. Amplification may Amplification; RAF inhibitors predict resistance to mutant-specific Rearrangement

RAF inhibitors (like vemurafenib).

RARA Transloactions predict sensitivity to Rearrangement ATRA, Arsenic

ATRA and arsenic

RBI May be prognostic or diagnostic in BiaUeiic Inactivation CDK inhibitors

some tumor types. Loss may predict

resistance to CDK inhibitors.

RET Mutations and fusion may predict Mutation; Sorafenib, vandetinib, sensitivity to RET inhibitors Rearrangement RET inhibitors

ROS1 Translocations predict sensitivity to Rearrangement Crizotinib

crizotinib.

RUNX1 May be prognostic / diagnostic in Rearrangement

some hematologic maiginaneies.

SMAD2 May be prognostic in some GI BiaUeiic Inactivation

tumors

SMAD4 May be prognostic in some GI BiaUeiic Inactivation

tumors

SMARCA4 Inactivation may predict sensitivity BiaUeiic Inactivation HDAC

to HDAC inhibitors Gene Rationale Types of recurrent Examples of alterations Therapeutic Agents

SMARCB1 Inactivation may predict sensitivity Biallelic Inactivation CDK inhibitors

to CDK Inhibitors, Hedgehog Vismodegib, Hedgehog Inhibitors, and/or HDAC Inhibitors inhibitors

HDAC inhibitors

SMO Mutations may predict sensitivity to Mutations Vismodegib, hedgehog hedgehog inhibitors inhibitors

STK11 Biallelic inactivation may predict Biallelic Inactivation Everlolims,

sensitivity to MTOR inhibitors. Temsirolimus, MTOR Biallelic inactiavtion may predict inhibitors sensitivity to SRC inhibitors, FAK Dasatinib, src inhibitors inhibitors, or phenformin. FAK inhibitors

Phenformin

SYK Activating mutations may predict Mutation SYK inhibitors

sensitivity to Syk inhibitors

TET2 Prognostic in MDS Mutations

TMPRSS2 Fusion with ERG shown to potentiate Rearrangement PARP Inhibitors

sensitivity to PARP inhibitors.

Diagnostic in prostate cancer

TP53 Biallelic inactivation or mutation Biallelic Inactivation Wee I inhibitors

may be prognostic in some tumor Chkl inhibitors types. They may also predict kevetrin sensitivity to some cell cycle APR-246 inhibitors and p53 specific gene nutlins

therapies or immunotherapies. May gene therapy signal the presence of a germline

mutation.

TSC1 Biallelic inactivation may predict Biallelic Inactivation Everolimus,

sensitivity to MTOR inhibitors Temsirolimus, MTOR inhibitors

TSC2 Biallelic inactivation may predict Biallelic Inactivation Everolimus,

sensitivity to MTOR inhibitors Temsirolimus, MTOR inhibitors

VHL Ma signal the presence of a Biallelic Inactivation

germline mutation.

WT1 May signal the presence of a Biallelic Inactivation

germline mutation.

XPOl Mutations may predict sensitivity to Mutation SINE agents

small molecule selective inhibitors of

nuclear export (SINE)

[0Θ264] Supplementary Table 6. Summary statistics for TARGET in 511 patient exomes.

This table includes summary statistics for the number of alterations observed in genes represented in TARGET, the Cancer Gene Census (CGC), cancer pathways or modules from MSigDB, and COSMIC. The set difference for TARGET and CGC is also included. It reveals 20 genes with potential clinical relevance included in TARGET that are not currently in the CGC.

[00265] Supplementary Table 7. Details on individual patient cases. This table includes information about tumor type, tissue type (FFPE or frozen), protocol, and mean target coverage for prospectively studied patient cases.

5 17

[00266] Supplementary Table 8. Levels of Evidence. To assign the strictest possible definition of evidence linking an alteration to a clinical action for each given variant, all highest scoring variants are curated with the aim of assigning each a level (A through E) depending on the category of action. Inferential associations are based on homology, computational data, structural information, or pathway involvement. Those that do not meet criteria for any level of evidence are considered unknown variants. ATEGO

LEVEL A LEVEL B LEVEL 1> LEVEL E

There is a There is There is There is There is an

FD./ validated limited clinical clinical inferential ed association evidence (early evidence for an evidence for an association les between this or conflicting association association between this alteration and data) for an between this between this alteration and response/resista association alteration and alteration and response/resista nee to this between this response/resista response/resista nee to this agent for this alteration and nee to this rice to this agent

indication response/resista agent in agent

nee to this

agent in this e^■ This alteration There is There is There is There i a ies i is used or has

been used as an evidence (early evidence for an evidence for an

or conflicting association association between this criterion for data) for an between this between this alteration and clinical trials of association alterat on and alteration and response/resista this agent or between this response/resista response/resista nee to this class of agents alteration and nee to this nee to this agent or class response/resista agent or class agent or class of agents rice to this of agents in of agents

agent or class another tumor

of agents in type ONLY

There is a There is

i

evidence for an

between this association

alteration and between this

prognosis in alteration and

this tumor type prognosis in

this tumor type

There is a There is

evidence for an

between this association

alteration and a. between this

diagnosis alteration and a

diagnosis

[0Θ267] Supplementary Table 9. Curation results for somatic alterations nominated by PHIAL. For the 16 patients studied prospectively, this table includes curated details about the clinically relevant alterations nominated by PHIAL. This includes information about the alteration type, allelic fraction, copy number segment mean, curation references, and rationale for the assigned level of evidence. Patient Information Alteration Overview Additional Alteration Data

Nijra

Allelic er of Segiue

Variant Altera tt Covers fracti Probe nt

Patient Gene on Mean

1 DFC1.11 -104,02- Prostate JAK3 Missense Mutati P.RS70W 138 0.07 NA NA Tumor Cancer on

2 DFCT.i 1-304.02- Prostate MET Missense Mutati P.H209Y 235 0.02 N^'A NA Tumor Cancer on

3 DFC1.11-304.03- Lung ATM Frame_Shift_Ins p.K208fs 39 0.36 NA NA Tumor Adenocarcino

ma

4 DFCI.i S -104.03- Lung KRAS Missense Mutati P.A146V 248 0.61 NA NA Tumor Adenocarcino on

ma

5 DFC1.11 -104,03- Lung STKi l Frame Shift De p.G279fs 23 0.48 NA NA Tumor Adenocarcino i

ma

6 DFCI.11-304.04- Leiomyosarco SYK Missense_Mutati p.P336T 363 0.08 NA NA Tumor ma with on

Myxoid

Fe tures

7 DFC1.11 -104,04- Leiomyosarco TP53 Frame Shift De p.L330is 70 0.23 NA NA Tumor ma with i

Myxoid

Features

8 DFCL i i -104.05- Gastric CTNNB1 Missense Mutati p.D32N 82 0.05 NA. NA Tumor Adenocarcino on

ma

9 DFC1.11 -104.05 - Gastric P3K3CA Missense Mutati p.RSSQ 234 0.03 NA NA Tumor Adenocarcino on

ma

1 DFCl.i 1-304.06- Urothelial CR L Copy Number Amplified NA NA 33 3.3003

0 Tumor Carcinoma

1 DFCL l i-104.06- Urothelial TP53 Frame Shift De p.F2121¾ 38 0.68 NA NA i Tumor Carcinoma ί

i DFCL l Ϊ -104.07- Leiomyosarco TP53 Copy Number Deleted N^'A NA ⁵ -2.31485

2 Tumor ma

1 DFCl.i 1 -104.08- Lu g F.GFR Missense Mutati P.L858R 287 0.13 NA NA

3 Tumor Adenocarcino on

ma

1 DFCl.i 1-304.08- Lung 1P53 Nonsense Mutat p.C124* 204 0.14 N^'A NA

4 Tumor Adenocarcino ion

ma

1 DFCI. i l- Pleomorphic RBI Copy Number Deleted NA NA 121 -1.072 5 104.09 POST Liposarcoma

i DFCI. l l -104. l l- Follicular EGFR Missense Mutati p.V1097i 151 0.03 NA. NA

6 Tumor Dendritic Cell on

Sarcoma

1 DFCl.11 -104.11- Follicular ETV6 Missense Mutati P.R309W 781 0.01 NA NA 7 Tumor Dendritic Cell on

Sarcoma

1 DFCL 11 -304.11- Follicular MDM2 Copy Number Amplified NA NA 106 2.0052

8 Tumor Dendritic Cell

Sarcoma

1 DFCl.i l -104. i l - Follicular FKT5IA Frame Shift De p.L387fs 133 0.21 NA NA

9 Tumor Dendritic Cell ^■

Sarcoma

2 DFCl.i i-I04. i3- Prostate AR Copy Number Amplified NA. NA 17 5.0875 0 Tumor Cancer

2 DFC1.J 1-104.13- Prostate AR In Frame Dei p.Q93 del 243 0.03 NA NA 1 Tumor Cancer

DFCL l i-104.13- Prostate TP53 Missense Mutati p.S241Y 33 0.73 NA NA Tumor Cancer on

M-i i-001 -3- Melanoma J3RAF Missense Mutati P.V600E 117 0.52 NA. NA

3 Tumor on Patient Information Alteration Overview Additional Alteration Data

umb

Allelic er of Segiue

Tumor Variant Aicerats Covers fracti Probe nt

Patient Type Gene Qassiiieation on Mean

2 M-11-001-3-- Melanoma ERBB4 Missense Mutati P.D813N 120 0.23 NA NA 4 Tumor on

2 M-i ί -001-3- Melanoma GNAS Missense Mutati P.E114K 130 0.36 N^'A NA 5 Tumor on

M- 3 3 -001-3- Melanoma MAP2K1 Missense_Mutati P.Q56P 239 0.02 NA NA Tumor on

M-i i -001-3- Melanoma PTEN Copy Number Deleted NA NA 21 -1.8793 η Tumor

Nerve Sheath hgl Malignant CDKN2 Copy Number Deleted N^'A N 1 3 -1.1594

8 9-Tumor Peripheral A

Nerve Sheath

Tumor

Nerve Sheath hgl Malignant CDKN2 Copy Number Deleted NA NA 11 -1.1 594

9 9-Tumor Peripheral B

Nerve Sheath

Tumor

3 Nerve Sheath hgl Malignant MTOR Missense Mutati P.I.1433S 430 0.83 NA NA 0 9-Tumor Peripheral on

Nerve Sheath

Tumor

3 Nerve Sheath hgl Malignant SMARC Nonsense Mutat p.R40* 403 0.56 NA NA i 9-Tumor Peripheral Bi ion

Nerve Sheath

Tumor

3 Nerve Sheath hgl Malignant SMARC Frame Shift De p.R316fs 160 0.26 NA NA

2 9-Tumor Peripheral Bi

Nerve Sheath

Tumor

3 Osteosarcoma hgl Osteosarcoma P1K3CA Missense Mutati p.E545D 180 0.38 NA NA 3 9-Tumor on

3 Osteosarcoma hgl Osteosarcoma TP53 Missense Mutati p.R248Q 79 0.53 NA. NA 4 9-Tumor on

3 pal2 Glioblastoma Glioblastoma CDK4 Copy Number Amplified NA NA 59 4.3814 5 -Tumor

3 pat2 Glioblastoma Glioblastoma KIT Copy Number Amplified NA NA 194 2.6432

6 -Tumor

3 par.2 Glioblastoma Glioblastoma P GFRA Missense Mutati p.V309F 609 0.76 N^'A NA -Tumor on

3 UnknownPrimary Squamous CDKN2 Copy Number Deleted NA NA 73 -1.0728 8 04-Tumor Cell

Carcinoma of

Unknown

Primary

3 UnknownPrimary Squamous CDK 2 Copy Number Deleted NA. NA 73 -1.0728 9 04-Tumor Cell B

Carcinoma of

Unknown

Primarv

4 UnknownPrimary Squamous FGFR2 Missense Mutati p.G583W 156 0.04 NA NA 0 04-Tumor Cell on

Carci oma of

Unknown

Primarv

4 Unkno nPnmafy St!uamous TP53 Missense Mutati p.G244A 105 0.50 NA. NA 1 04-Tumor Cell on

Carcinoma of

Unknown

Primary Supp. Table 9 Curated events

(continued)

Alteration Curation Data

Highest Levei

of Evk!ejiee

for Predictive Se!ected Oinicai

Categories Se!eeted References (PMID or abstract) Trial IDs Rationale

A 20573926 Mutations targetabie with TKis (both

FDA approved and novel). Other mutations predict resistance to TKis. Amplification associated with response to anti-EGFR Abs in colon cancer. Amplification also associated with resistance to TKis in some cancers. Rearangement is prognostic in GBM, HNSCC

D 22965952, 2046WH. 20975744. 21799033, Bialieiic maciivation or mutation may be

20107315, 22446188, 22965953 prognostic in some tumor types. They may also predict sensitivity to some cell cycle inhibitors and p53 specific gene therapies or immunotherapies. May signal the presence of a germline mutation.

D 21955141, 22237022 CT01320592 May be prognostic or diagnostic in some tumor types. Loss may predict resistance to CDK inhibitors.

E 18478265, 22980975 Mutations targetabie with TKis (both

FDA approved and novel). Other mutations predic t resistance to TKis. Amplification associated with response to anti-EGFR Abs in colon cancer. Amplification also associated with resistance to TKis in some cancers. Rearangement is prognostic in GBM, HNSCC

Unknown Diagnostic in prostate cancer

D 23165797, 23400593, 19996219 Amplification may predict sensitivity to

Nutlins and MDM2 inhibitors

Unknown Deletion is prognostic in GBM

D 21859989 Amplification may predict resistance to androgen deprivation in prostate cancer and may predict sensitivity to second generation androgen deprivation or direct androgen inhibitors

Unknown Amplification may predict resistance to androgen deprivation m prostate cancer and may predict sensitivity to second generation androgen deprivation or direct androgen inhibitors

D 22965952, 20463003, 20975744, 21799033, Bialieiic inactivation or mutation may be

20107315, 22446188, 22965953 prognostic in some tumor types. They may also predict sensitivity to some cell cycle inhibitors and p53 specific gene therapies or immunotherapies. May signal the presence of a germline mutation.

A 22356324 Mutations predict sensitivity to RAF

inhibitors. Amplification may predict resistance to MBK inhibitors.

E 22889873 Mutations may predict sensitivity to

Lapatinib and other anti-EGF family inhi itors

Unknown Mutations may be diagnostic of tumors arising in McCune-AJ bright syndrome, and may be targetabie with JAK inhibitors

D 1991 5144, 21383288 Mutations predict resistance to R F- and

MEK- inhibitor Alteration Ciiraiso!i Data

Highest Levei

of Evk!ejiee

for Predictive Se!ected Oinicai

Categories Selected References (PMID or abstract) Trial IDs Rationale

A 22588880, 23136191 , 21998291 CT00877773 Biallelic inactivation may predict sensitivity to PI3K pathway inhibitors— P13K inhibitors, AKT inhibitors, and MTOR inhibitoB. Biallelic inactivation may predict resistance to anti-E T^'K therapy, including cetuximab, anti-EGFR TKIs, and trastuzumab and lapatinib, Biallelic inactivation may predict sensitivitv to PARP inhibitors

D 21262917, 21173237, 2273 1607, 21278246, Biallelic inactivation may predict

20534551, sensitivity to CDK4/6 inhibitors. https ://meeiinglibrary. asc o. org'content/95431 - 114

D 23262917, 21173237, 22711607, 21278246, Biallelic inactivation may predic t

20534551 , sensitivity to CDK4/6 inhibitors. littps ://meetmgiibrary . asco. org/con tent/95431- 114

E 21210909, 20190810, 17360675, 18812319 Activating mutations may predict sensitivity to MTOR inhibitors.

Secondary mutations may predict resistance to MTOR inhibitors

D 21654818, 19^''^'' i ¾6 inactivation may predict sensitivity to

CDK Inhibitors, Hedgehog Inhibitors, and/or HDAC Inhibitors

D 21654818, 19221586 Inactivation may predict sensitivity to

CDK Inhibitors, Hedgehog Inhibitors, and/or HDAC Inhibitors

A 22949682, 21750239, 2.1998291 , 2.2588880, CT01708161 Mutations may predict sensitivity to

20453058, 22162589 PI3K pathway inhibitors - PI3K

inhibitors, AKT inhibitors, and MTOR inhibitors. Mutations may predict resistance to anti-RT therapy, including cetuximab, anti-EGFR TKIs, and trastuzumab and lapatinib

D 22965952, 20463003, 20975744, 21799033. Biallelic inactivation or mutation may be

20107315, 22446188, 22965953 prognostic in some tumor types. They may also predict sensitivity to some cell cycle inhibitors and p53 specific gene therapies or immunotherapies. May signal the presence of a germline mutation.

C 23569312, 22711607 Amplification may predict sensitivity to

CDK4/6 inhibitors.

Unknown Mutations targetable with TKIs (both

FDA approved and novel). Secondary mutations predict resistance to TKIs. Amplification also associated with, resistance to TKIs.

E 22718859 Alterations may predict sensitivity to imatinib and other TKIs

D 22711607, 21 2.78246, 20534551, Biallelic inactivation may predict littps ://meetinglibrary. asco.org' ontent/9543 Ϊ-- sensitivity to CDK4/6 inhibitors.

1 34

D 2273 1607, 21278246, 20534551, Biallelic inactivation may predict tips://meeiinglibrai ^asco.org/content/95433 - sensitivity to CDK4/6 inhibitors.

E 17525745, 23468082 Alter tions may predict sensitivity to

FGFR inhibitors Alteration Curation Data

Highest Level

of Evidence

for Predictive Se!ected Clinical

Categories Selected References (PMID or abstract) Trial IDs Rationale

D 22965952, 20463003, 20975744, 217990¾ ¾, Biailelsc inactivation or mutatiosi may be

20107315, 2244618S, 22965953 prognostic in some tumor types. Hey may also predict, sensitivity to some cell cycle inhibitors and p53 specific gene therapies or immunotherapies. May signal the presence of a germiine mutation.

COSMIC COSMIC total

Tumor Reference overlapping alterations In

allele allele mutations gene UniProt Region

(2)|p.?(2)|p.L10 N141

del(2)|p.D6 A43del(l)

!p.E9 S47dei(l)|p.Q28

Q61del(1)|p.A20 l

51d (l)jp,A20 141

del(l)jp.Dll Y142>H

(i)ip.H24 G38del(l)|p

.S29 H36dei(!)jp.Y30

A97del(1)|p.A20 A8

0del(l)|p.Q28 A43del

(l)|p.E15 I140>V(l)!p

.D17 P128dei(l)jp.H2

4 M131delfi)ip.L7 11

40del(1)!p.K19 ΥΊ42

>V(l)|p.A20_L148del

iDip.V22 A80del(l)|p

.W25 I35dei(l)|p.V22

G80>NNN N(l)|p.A

5 I35del(l)|p.A20 Ql

43del(l)jp.A13 I51d

e{{l)!p„D32de{{l)!p„S2

3 1140del(l)|p.Ml A

87del(l)|p.W25 S33d

el(l)|p.V22 T102del(l

)!p.S23 A39dei(l)ip.A

21 A80del(l)ip.D6 11

40del(l)|p.Q28_I140d

el(l)!p.E9 A80del(l)jp

.M14 S45del(l)|p.M8

G50del(l)|p.A5 G80

>(l)!p.D32 H36>D(!)

!p.P16 K133del(l)ip.

A5 T59dei{l)jp„A20 I

35del(l)|p,Ml^' V173d

ei(l)|p.A5 R90del(l)i

P.V22 Y64delfl)!p.M

8 A80def(l)|p.E9 114

0de1(l)ip.T332 S33ins

S(l)|p.Y30 T40del(l)|

p.Ml T42del(l)jp.A5

Q143>E(l)|p.A5 Q7

2del(l)ip.Q28 D32>H

(l)|p.Y30 A80del(1)!p

.D32fs*9(l)|p.D6 K13

3del(l)ip.A5 T42del(l

)!p.A5 D144>D(l)|p.

A5 T40dei(!)jp.D17

EXAMPLES

[00268 J The following examples are given for the purpose of il lustrating various embodiments of the mvention and are not meant to limit the present invention in any fashion. The present examples, along with the methods described herein are presently representative of preferred embodiments, are exemplary, and are not intended as limitations on the scope of the invention. Changes therein and other uses which are encompassed within the spirit of the invention as defined by the scope of the claims will occur to those skilled in the art.

[00269] Example 1 : Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine

[00270] Translating whole-exome sequencing (WES) for prospective clinical use may have an impact on the care of patients with cancer; however, multiple innovations are necessary for clmical implementation. These include rapid and robust WES of DNA derived from formalin- fixed, paraffin-embedded tumor tissue, analytical output similar to data from frozen samples and clinical interpretation of WES data for prospective use. Here, Applicants describe a prospective clinical WES platform for archival formalin-fixed, paraffin-embedded tumor samples. The platform employs computational methods for effective clinical analysis and interpretation of WES data. When applied retrospectively to 51 1 exomes, the interpretative framework revealed a 'long tail' of somatic alterations in clinically important genes. Prospective application of this approach identified clinically relevant alterations in 15 out of 16 patients. In one patient, previously undetected findings guided clinical trial enrollment, leading to an objective clinical response. Overall, this methodology may inform the widespread implementation of precision cancer medicine. [00271] Massively parallel sequencing approaches such as WES have elucidated the landscape of genetic alterations in many tumor types and revealed biological insights relevant to clinical contexts (Garraway, L.A. & Lander, E.S. Cell 153, 17-37 (2013)). The increased practical availability and decreased cost of tumor genomic profiling has generated opportunities to test the 'precision medicine' hypothesis in clinical oncology (Garraway, L.A. J. Clin. Oncol. 31, 1806-1 814 (2013)). In principle, knowledge of alterations in the coding regions of all genes may inform immediate treatment choices and further therapeutic discovery efforts (Garraway, L.A. & Jamie, P. A. Cancer Discov. 2, 214-226 (2012)).

[00272] Most prospective clinical genotyping efforts have used 'hotspot' genotyping (Thomas, R.K. et al Nat. Genet. 39, 347-351 (2007); MacConaili, L.E, et ai. PLoS ONE 4, e7887 (2009); Dias-Santagata, D. ,-/ ai. EMBO Mel, Med. 2, 146-158 (2010).) or targeted sequencing panels of clinically relevant genes using either fresh frozen or formalin-fixed, paraffin-embedded (FFPE) tissue (Wagle, N. et ai. Cancer Discov. 2, 82-93 (2012); Lipson, D, et al Nat. Med. 18, 382-384 (2012); Beitran, H. et al Eur. Urol 63, 920-926 (2013)). Pilot studies that apply research-grade massively parallel sequencing technology in focused clinical settings have also been reported (Wagle, N. et al. Cancer Discov. 2, 82-93 (2012); Roychowdhury, S. et al. Sci. Transl. Med. 3, 11 1 ra 121 (2011); Craig, D.W. et al. Mol. Cancer Ther. 12, 104-1 16 (2013); eriek, M. et ai. BMC Med. Genomics 4, 68 (201 1)), although production-scale efforts have not been demonstrated. Multiple challenges to widespread clinical WES implementation remain. One challenge involves rapidly generating high-quality WES data from archival FFPE tumor material (Goetz, L., et ai. J. Am. Med. Assoc. 3Θ9, 37-38 (2013)). Another involves clinically interpreting WES data for prospective use that maximizes clinical and biological exploration. A third involves developing a system to interrogate plausibly actionable variants of uncertain significance. Overcoming these challenges should allow rigorous assessment of the value of WES to guide clinical decision making and inform selected experimental follow-up.

[00273] Here, Applicants describe an approach to generate high-quality WES data from archival tumor material and validate WES data from FFPE tumor samples with corresponding WES data from frozen samples. Applicants also present a heuristic algorithm that interprets the resulting data for clinical oncologists and establish the clinical applicability of this interpretation algorithm in a retrospective cohort of 511 cases. Prospective application of this platform in patients with a range of tumor types indicates that this approach can be used for both biological discovery and clinical trial enrollment. This approach may therefore facilitate widespread application of WES for precision cancer medicine studies.

[00274] RESULTS: WES of FFPE samples

[0Θ275] To produce WES data for clinical use, robust sequencing data must frequently be generated from small quantities of archival FFPE tissue. To test this, Applicants extracted DNA from 99 FFPE samples using the FFPE extraction protocol (Supplementary Table 1 and Methods). A comparison of standard WES metrics (Fisher, S. et at. Genome Biol, 12, Rl (2011)) with 768 non-FFPE samples (394 whole blood, 367 frozen, 7 cell line) sequenced in parallel demonstrated no significant differences independent of input DNA quantity (P > 0.05, Mann- Whitney i/-test; Fig. la-c and Supplementary Table 1). Applicants' lowest successful WES attempts were achieved with 13.6 ng and 16 ng DNA derived from non-FFPE and FFPE tissue, respectively,

[0Θ276] Moreover, improvements in process design (Methods) combined with the 'with-bead' approach (Fisher, S. et al. Genome Biol. 12, Rl (2011)) yielded a time to exome data delivery of 17.4 ± 2.2 d (median ± s.d.; 25th and 75th percentiles 14.3 and 18.6, respectively) for FFPE samples received as DNA and 20.1 ± 2.4 d (median ± s.d.; 25th and 75th percentiles 17.5 and 21.2, respectively) for samples received as FFPE tissue blocks (Supplementary Table 2). This turnaround time is compatible with several clinical oncology applications.

[00277] Applicants next assessed WES data using even smaller amounts of input DNA, Here, Applicants achieved >80% of targeted nucleotides from the hybrid selection reaction, even when Applicants used only 1 ng of input DNA; Applicants saw equivalent results with DNA derived from FFPE and non-FFPE tissue. However, to meet Applicants' metrics of >80% targets with at least 2Qx coverage and >100x mean target coverage across the exome, a disproportionate amount of additional sequencing was required owing to an increase in the fraction of duplicate molecules in the library.

[00278] FFPE and fresh frozen samples yield comparable WES results

[0Θ279] Next, Applicants sought to compare WES data generated from FFPE and frozen material. Applicants assessed WES data from 1 1 lung adenocarcinomas for which tumor and adjacent normal tissue were available from matched FFPE (aged <5 years, Supplementary Table 3 and Figs, 6 and 7) and frozen (Fig. 2a) samples. First, Applicants applied Applicants^' standard mutation detection pipeline on the tumor-normal pairs (Methods) and considered the concordance of mutation calls observed in FFPE tumors that Applicants observed in frozen tumors and vice versa. Applicants did not expect identical data, given tumor heterogeneity (Gerlinger, . et al. N. Engl. J. Med. 366, 883-892 (2012)) and low allelic fraction nucleotide transition artifacts induced by the FFPE fixation process (Pao, W., et al. N, Engl. J. Med. 353, 1739-1741 (2005); Williams, C. et al. Am. J. Pathol. 155, 1467-1471 (1999); Spencer, D.H. el al. J. Mol. Diagn. 15, 623-633 (2013)). Moreover, the mean target coverage achieved for the FFPE tumor and adjacent tissue samples was 1.5-2 times that for the corresponding fresh frozen samples (Fig, 8); as a result, Applicants had increased power to detect mutations in FFPE samples compared to the fresh frozen samples (Cibulskis, . et al. Nat. Biotechnol. 31, 213-219 (2013)). Therefore, Applicants considered the subset of observed exonic mutations in FFPE tumor cases where the depth of coverage afforded sufficient power (>95%) to detect the mutation in two or more reads in the matched frozen tumor case and vice versa. For sufficiently powered sites, 91.5% (2,923/3,194, 95% confidence interval (CI) ± 0.97) of mutations in FFPE samples were validated in patient-matched frozen samples. Similarly, 91.0% (3,399/3,735, 95% CI ± 0.92) frozen mutations were validated in sufficiently powered FFPE samples (P = 0.47) (Fig. 2a-c and Supplementary Table 4). Because the mean target coverage in the FFPE cases was higher than in their fresh frozen counterparts, Applicants then obtained a random subset of reads from each case such that all sites had a maximum coverage of 90^x ('downsampling' Cibulskis, K. et al. Nat. Biotechnol. 31, 213-219 (2013)) and repeated the cross-validation exercise, in this scenario, Applicants' validation rates for FFPE to fresh frozen and fresh frozen to FFPE for sufficiently powered sites were 92.6% (2,811/3,036, 95% CI ± 0.93) and 91 .5% (3,340/3,651 , 95%> CI ± 0.90), respectively (Fig. 9a,b and Supplementary Table 4).

[00280] In both FFPE and fresh frozen cases from each patient, Applicants observed mutations for which there was insufficient power to detect that mutation in the validation cohort after downsampling (Fig. 9c and Supplementary Table 4). Demonstrative examples of mutations in FFPE samples that could not be validated in fresh frozen counterparts are provided in Figs. lOa-c. Overall, these results suggested that the ability to detect base mutations that were sufficiently powered was equivalent regardless of whether frozen or FFPE tissue-derived genomic DNA was used for WES. [00281] Applicants also examined the chromosomal copy number patterns evident in WES data from frozen and FFPE tumor DNA in the 11 lung adenocarcinomas. In one representative patient, copy ratios for matching exons in FFPE and frozen sample data correlated (r = 0.89, P < 0,0001, Pearson's correlation; Fig. 2d,e). This correlation held across ail 1 1 cases, representing 1,338,859 exons (r² = 0.79, P < 0.0001, Pearson's correlation; Fig. 2f), Thus, WES data obtained from FFPE tumor DNA are comparable to fresh frozen sample WES data and may equally be used to measure global chromosome copy number information.

[00282] Clinical analysis and interpretation of WES data

[0Θ283] Having demonstrated robust WES using FFPE tumor-derived DNA, Applicants next sought to integrate this methodology into a broader framework for clinical interpretation of somatic alterations. Applicants reasoned that a heuristic (rule-based) approach that incorporated prior clinical and scientific knowledge might offer a useful set of organizing principles. By using primary literature, manual curation and expert opinion, Applicants generated a database of tumor alterations relevant for geiiomics-driven therapy (TARGET), a database of genes that may have therapeutic, prognostic and diagnostic implications for patients with cancer (Fig, 3b, Supplementary Table 5 and Methods). Applicants integrated the resulting 121 TARGET genes with existing open-source resources to create a series of rules that (i) sort each somatic variant by clinical and biological relevance, (ii) link TARGET genes with additional biologically significant pathways and gene sets and (iii) demote variants of uncertain significance. Thus, the resulting analytical algorithm used precision heuristics for interpreting the alteration landscape (PHIAL) (Fig. 3a-d and Methods). Beyond annotating variants, PHIAL applies rules that rank variants on the basis of clinical and biological relevance to computationally sort a patient's somatic variants.

[0Θ284] Applicants assessed the functionality of PHIAL using 51 1 patient cases from six prior WES studies (Imieiinski, M. et al. Cell 150, 1 107-1120 (2012); Banerji, S. et al. Nature 486, 405-409 (2012); Hodis, E. et al. Cell 150, 251-263 (2012); Barbieri, C.E. et al. Nat. Genet. 44, 685-689 (2012); Stransky, N. et al. Science 333, 1 157-1160 (201 1); Lohr, J.G. et al. Proc. Natl Acad. Sci. USA 109, 3879-3884 (2012)). Analysis tools (Methods) yielded 258,226 somatic alterations in protein-coding genes, of which 135,903 were nonsynonymous. Of these, PHIAL identified 1,842 somatic alterations in genes linked to clinical actions (TARGET genes) for 80% (408/511) of the patients (Fig. 3e). Additional descriptive statistics regarding altered genes per patient, stratified by inclusion in databases explored in PHIAL, are available in Supplementary Table 6. PEDAL identified known and highly recurrent actionable findings across this patient cohort. It also revealed a long tail of TARGET gene alterations present in small patient subsets that did not reach statistical significance in the individual cohort studies but may have immediate clinical ramifications for individual patients (Fig. 3f). Specifically, 39% (201/511) of the cases had alterations in at least one TARGET gene that was somatically altered in <2% of the overall cohort. This finding was reminiscent of similar long-tail alteration distributions observed for driver genes in cancer (Garraway, L.A. & Lander, E.S. Cell 153, 1 7—37 (2013)).

[00285] As a major near-term goal of precision cancer medicine is to use genetic information to inform clinical trial enrollment, Applicants also systematically queried ClinicalTriais.gov, a centralized registry of publicly and privately supported clinical studies worldwide, for oncology clinical trials linked to TARGET genes. The number of clinical trials including a TARGET gene in the title, the strictest means of identifying clinical trials with a genomic emphasis, grew steadily between 2005 and 2012 (Fig, 3g).

[0Θ286] WES and clinically actionable events across cancers

[00287] To pilot prospective sequencing and clinical interpretation, Applicants performed WES and PHIAL in 16 patients with a range of advanced cancers (Fig. 4a). WES data for 3 of these 16 patients predated the WES protocol described herein but were included to assess PH IAL output. WES data from all patients in the rapid sequencing protocol met Applicants' quality control parameters irrespective of tissue processing type (Supplementary Table 7). By completion of the pilot period, time from sample receipt through data delivery was 16 d.

[00288] For these 16 patients, PHIAL revealed 29 unique TARGET genes in the 'Investigate Clinical Relevance' category (median 2, range 0-5). Although, by definition, alterations in TARGET genes may have implications for clinical decision making, their actual clinical relevance requires case-by-case evaluation in real time. To facilitate this, Applicants manually curated every alteration ranked as investigate Clinical Relevance by PHIAL to include up-to-date knowledge from databases, literature and computational algorithms. Applicants generated a standardized, structured annotation for each alteration (Supplementary Note) and assigned a level of evidence to each potential clinical action based on that alteration. These levels of evidence (Supplementary Table 8) included predictive, prognostic and diagnostic categories and encompassed validated indications, preclinical evidence and analytical associations. [00289] Following curation and assignment of levels of evidence, Applicants identified 41 clinically relevant alterations in 15 out of 16 patients. These included standard-of-care findings, such as an EGFR^l*^~'gR mutation in lung adenocarcinoma linked to epidermal growth factor receptor (EGFR) inhibitors (predictive for US Food and Drug Administration (FDA)-approved therapies, level A), and PIK3CA alterations that are entry criteria for clinical trials (predictive for therapies in clinical trials, level A). 46.3% (19/41) of these alterations were based on preclinical evidence for the association of the alteration with response or resistance to FDA-approved therapies or therapies in clinical trials (level D) (Fig. 4b and Supplementary Table 9).

[00290] Applicants identified multiple unexpected clinically relevant findings in genes not well characterized for the corresponding tumor type. For instance, Applicants observed CRKL amplification in a patient with metastatic urothelial carcinoma (Fig. 11 ); this alteration has been predicted to confer resistance to EGFR inhibitors ( Cheung, H.W. et al. Cancer Discov, 1, 608- 625 (201 1)) and sensitivity to Src inhibitors (Natsume, H. et al. J Trans!. Med. 10, 97 (2012)) in preclinical studies but had not previously been described in urothelial carcinoma. To accommodate new TARGET genes emerging with future findings, Applicants have made TARGET publically available online (http://www.bioadinstitute.org/cancer/cga/targei) and encourage commuii ity contrib u lions .

[00291] The use of WES in clinical decision making

[00292] Applicants used the prospective WES framework for clinical decision making in one demonstrative case. A patient with metastatic lung adenocarcinoma underwent standard clinical genetic testing that revealed wild-type EGFR, KRAS (codon 12 and 13) and ALK status. Mass spectrometry testing of 471 alterations in 41 genes (MacConaili, L.E. et al. PLoS ONE 4, e7887 (2009)) revealed an STK11 frameshift deletion. Applicants started the patient on carboplatin, paclitaxel and bevacizttmab (Fig, 5a). In parallel, Applicants applied the clinical WES platform on the FFPE metastatic tumor sample and germline peripheral blood. PHIAL nominated a KRAS^{A t'}^ mutation as clinically relevant, along with alterations in STK11 (identical to other testing) and ATM (Fig. 5a and Supplementary Table 9). KR/lS^{Ai 46v} is a known activating mutation, although it is possibly less potent than the codon 12 and 13 mutations (Janakiraman, M, et al. Cancer Res. 70, 5901-5911 (2010)). Although activating KRAS mutations are found in 15-30% of all patients with non-small-cell lung cancer (NSCLC) and commonly in conjunction with STK11 loss (Carretero, J. et al. Cancer Ceil 17, 547-559 (2010)), this specific KRAS alteration has not been reported in NSCLC (Imielinski, M. et al. Cell 150, 1 107-1120 (2012); Forbes, S.A. et al. Nucleic Acids Res. 39, 1)945 1)950 (201 1); Ding, L. et al. Nature 455, 1069- 1075 (2008); Govindan, R. et al. Cell 150, 1121-1134 (2012)). Applicants confirmed KH4S^U6V using the same FFPE tumor sample in a clinical lab that met Clinical Laboratory Improvement Amendments (CLIA) standards (Knight Diagnostic Laboratories, Oregon), and then returned the data to the patient's oncologist. After rapidly progressing on combination chemotherapy (Fig. 5b), the patient was enrolled in a phase 1 clinical trial of a cyclin-dependent kinase 4 (CD 4) inhibitor (LY2835219) on the basis of preclinical data (level D) implicating a synthetic lethal relationship between activated KRAS and CDK4 (ref. 33). The patient achieved stable disease (per response evaluation criteria in solid tumors (RECIST) 1.1 criteria; 7.9% reduction in tumor volume compared to baseline) and was on therapy for 16 weeks (Fig. 5b, c). Of note, this was the patient's best and only clinical response to any cancer-directed therapy,

[00293] To maximize the potential of clinical WES, Applicants also implemented a procedure to generate experimental evidence for selected level E (inferential association) alterations. An exemplary case involved WES in a patient with metastatic castration-resistant prostate cancer that harbored an R870W missense mutation in the gene encoding Janus kinase 3 (JAK3) (Fig. 5d). Activating mutations in JAK3 have been described in hematological malignancies (Levine, R.L. Curr. Top. Microbiol. Immunol. 355, 119-133 (2012)), and JAK3 inhibitors are available clinically, including the FDA-approved agent tofacitinib. J4iD^{R870 v} has not been previously identified in cancer, and the function of this mutation is unknown,

[0Θ294] The crystal structure of JAK3 demonstrates that the arginine at residue 870 directly coordinates the phosphate group of the primary activating tyrosine phosphorylation site (pTyr981) (Boggon, T.J. et al. Blood 106, 996-1002 (2005)) (Fig. 5e). This interaction is expected to pull JAK3 into the active conformation. Indeed, residue 870 is conserved as an arginine or lysine in virtually all JAKs. Given the functional importance of this residue. Applicants hypothesized that this alteration could, in principle, be activating. Thus, Applicants categorized this alteration as level E (Supplementary Table 9).

[0Θ295] Applicants used a Ba/F3 system to examine the activity of JAK3 ^,'^iJ* as compared to wild-type JAK3 and a known activating mutation in JAK3, A572V (ref. 36). Ba/F3 cells are mouse hematopoietic cells dependent on interieukiii-3 (IL-3) for survival. Expression of some oncoproteins substitutes for IL-3 signaling, allowing for the growth of Ba/F3 cells in the absence of 1L-3. This system has been used extensively to characterize activating mutants of JAK3 in prior studies (Malinge, S. et al. Blood 112, 4220-4226 (2008)). Ba/F3 cells expressing J4iO^Rs'^0¾ did not achieve IL-3-independent growth following complete IL-3 withdrawal, in contrast to cells expressing a known JAK3 activating mutation (JAK3^{A5 ,2} ) or those growing in the presence of IL-3 (Fig. 5f). This suggested that J4iD^{R8 0 v} is unlikely to be an activating mutation and that JAK.3 inhibitors are unlikely to benefit this patient.

[00296] DISCUSSION

[00297] This study demonstrates that rapid WES can be applied to FFPE clinical samples and that robust WES analysis and interpretation can prospectively inform clinical trial enrollment. This approach incorporates new algorithms to identify clinically relevant alterations among numerous somati c events. Furthermore, real-time curation of nominated alterations assi gns l evels of evidence to the corresponding clinical actions for that alteration in that tumor type. In a proof- of-concept application, Applicants identified at least one clinically relevant alteration in 15 of 16 patients and showed how such findings can lead to clinical trial enrollment and biological discover}'.

[00298] Targeted sequencing of clinically relevant gene panels (containing hundreds of genes) have recently become possible from FFPE tumor samples (Wagle, N. et al. Cancer Discov. 2, 82-93 (2012)) and are increasingly used clinically. However, there are numerous advantages to clinical WES over targeted sequencing. First, as the spectrum of clinically actionable alterations grows (Garraway, L.A. .1. Clin. Oncol. 31, 1806 -1814 (2013)), targeted sequencing of particular genes is likely to be incomplete: the rapid pace of drug development linked to a growing number of clinically relevant genes will probably outpace the ability to alter targeted sequencing approaches in real time, while, as the same time, performing clinical WES becomes more facile and cost efficient. The completeness of clinical WES also enables longitudinal queries if new clinical trials open for previously unrecognized cancer genes not acted on therapeutically during the initial evaluation.

[00299] Furthermore, Applicants expect the volume of inferentially actionable or unknown- significance alterations will rise as more patient exomes emerge clinically. Clinical WES allows the generation of deeply annotated genomic data (linked to outcomes and responses) that could be mined to inform TARGET entries. Applicants recognize that the pace of cancer discovery will necessitate continual TARGET updates to ensure its relevance, and Applicants encourage input from the clinical and scientific community to expand and update its content for all to benefit. Methods to aggregate such data in a systems biology approach (Gonzalez-Angulo, A.M. et al. J. Clin. Oncol, 28, 2777-2783 (2010)) are being developed to foster functional and clinical follow- up (Yen, P. et al. Clin. Cancer Res. 19, 1894-1 901 (2013); Cerami, E. et al Cancer Discov. 2, 401-404 (2012)).

[00300 J There are ways to improve upon the framework. Efforts to further minimize the input DNA requirement and predict which samples yield successful WES will improve production- level sequencing. This process will, be enhanced by pathology review of clinical samples to enrich tumor DNA selection. Improvements in exome-derived copy number algorithms will better distinguish homozygous from heterozygous deletions in stromally admixed tumor samples. ntegration of additional profiling technologies (for example, transcriptome profi ling) will provide increasingly complex views of an individual's cancer and incorporate other changes (for example, epigenetic) that may have clinical relevance. In paral lel, efforts to demonstrate the utility of massively parallel sequencing platforms in larger prospective clinical settings are underway.

[00301] PHIAL is heuristic based; a probabilistic model that assesses alteration clonality with preclinical data may better inform the functional impact of WES findings for individual patients. Even with predictive models, sequencing will frequently identify previously uncharacterized alterations in known genes. Furthermore, relevant information about known genomic alterations is constant!)' changing, and the availabi lity of new therapies and clinical trials is in rapid flux. Because of this, alteration interpretation presently requires real-time manual curation, which requires dedicated and skilled resources that would benefit from crowdsourcing efforts such as those Applicants are establishing with TARGET and PHIAL.

[00302] Finally, rapid experimental validation of level E alterations to understand their clinical relevance will require large-scale innovations of scale to accelerate functional follow-up. Applicants' experimental efforts described here establish a priority biological evaluation system for one type of functional assessment. A flexible experimental follow-up system to comprehensively assess any alteration will need to be developed.

[00303] With the 'start-to-finish' approach for clinical WES described here, it may be possible to implement these methods widely and facilitate routine WES in clinical oncology. Once implemented, this will enable the prospective study of patients in trials to determine whether large-scale genomic profiling improves patient care and, ultimately, outcomes.

[0Θ304] Accession codes. WES BAM files for data from this study are deposited in dbGaP with accession codes phsOG0488 for lung adenocarcinoma cases and phs000694 for clinical cases.

[00305J METHODS

[00306] Patient samples. Tumor and germline samples used for this study were obtained under approved protocols from the Dana-Farber Harvard Cancer Center Institutional Review Board, the Peter MacCai lum Cancer Center Ethics Committee and the Massachusetts institute of Technology Committee on the Use of Humans as Experimental Subjects. Written informed consent was obtained from all subjects. Patient characteristics are described in Supplementary Table 7.

[00307] Rapid formalin-fixed, paraffin-embedded sequencing. Using industrial best practices in workflow design and a value-add approach, the standard exome workflow was modified to minimize touch points, handoffs and wasted process steps. Next, optimizations were made to the library construction and in-solution hybridization protocols to enable a 17-h hybridization reaction, 55 h shorter than the standard 72 -h hybridization reaction.

[00308] FFPE DNA extraction. Paraffin is removed from FFPE sections and cores using CitriSolv (Fisher Scientific) followed by ethanoi washes, and then tissue is lysed overnight at 56 °C, Samples are then incubated at 90 °C to remove D^'NA crosslinks, and extraction is performed using Qiagen's QIAamp DNA FFPE Tissue Kit.

[00309] Library construction. This was performed as previously described (Fisher, S. et al. Genome Biol. 12, Rl (201 1)) with the following modifications: initial genomic DNA input into shearing was reduced from 3 g to 10-100 ng in 50 μΕ of solution. For adaptor ligation, illumina paired-end adapters were replaced with palindromic forked adapters, purchased from Integrated DN A Technologies, with unique 8~base molecular barcode sequences included in the adaptor sequence to facilitate downstream pooling. With the exception of the palindromic forked adapters, the reagents used for end repair, A-base addition, adaptor ligation and library enrichment PGR were purchased from KAPA Biosciences in 96-reaction kits. In addition, during the postenrichment solid phase reversible immobilization (SPRI) bead cleanup, elution volume was reduced to 20 μ,Ε to maximize library concentration, and a vortexing step was added to maximize the amount of template eluted from the beads. Any libraries with concentrations below 40 ng/μΐ, as measured by a PicoGreen assay automated on an Agilent Bravo, were considered failures and reworked from the start of the protocol,

[00310] In-solution hybrid selection, In-solution hybrid selection was also performed as previously described (Fisher, S. et al. Genome Biol. 12, Rl (201 1)) with the following modifications to the hybridization reaction. Before hybridization, any libraries with concentrations >60 g^iL, as determined by PicoGreen, were normalized to 60 ng ,iiL, and 8.3 μΐ, of library was combined with blocking agent, bait and hybridization buffer. Any libraries with concentrations between 50 and 60 g/^L were normalized to 50 ng',uL, and 10.3 \ L of library was combined with blocking agent, bait and hybridization buffer. Any libraries with concentrations between 40 and 50 ng/ .L were normalized to 40 ng/''μϊ.,, and 12.3 uL of library was combmed with blocking agent, bait and hybridization buffer. Regardless of library concentration range, the same volume of blocking agent and bait previously described (Fisher, S. et al. Genome Biol. 12, Rl (201 1)) were used, and hybridization buffer volume was adjusted to equal the combined volume of library, blocking agent and bait. Finally, the hybridization reaction was reduced to 17 h with no changes to the downstream capture protocol.

[00311 ] Preparation of libraries for cluster amplification and sequencing. A fter post-capture enrichment, libraries were quantified using PicoGreen (automated assay on the Agilent Bravo), normalized to equal concentration on the Perki Elmer MiniJanus and pooled by equal volume on the Agilent Bravo. Library pools were then quantified using quantitative PCR (kit purchased from KAPA Biosystems) with probes specific to the ends of the adapters; this assay was automated using Agilent's Bravo liquid handling platform. Based on qPCR quantification, libraries were normalized to 2 nM and then denatured using 0.2 N NaOH on the Perkin-Elmer MiniJanus. After denaturation, libraries were diluted to 20 pM using hybridization buffer purchased from Iliumina.

[00312] Cluster amplification and sequencing. Cluster amplification of denatured templates was performed according to the manufacturer's protocol (Iliumina) HiSeq v3 cluster chemistr and flowcells, as well as Illumina's Multiplexing Sequencing Primer Kit, Flowceils were sequenced using HiSeq 2000 v3 Sequencing-by-Synthesis Kits and then analyzed using RTA v.1.12.4.2 or later. Each pool of whole-exome libraries was run on paired 76-bp runs, and 8 -base index sequencing read was performed to read molecular indices across the number of lanes needed to meet coverage for all libraries in the pool.

[0Θ313] D A assembly and quality control. Sequence data processing. Exome sequence data processing was performed using established pipelines at the Broad Institute. A BAM file was produced with the Picard pipeline (http://picard.sourceforge.net/), which aligns the tumor and normal sequences to the hgl 9 human genome build using illumina sequencing reads. The BAM was uploaded into the Firehose pipeline

(http://vvww .broadinstiMe.org/cancer/cga/Firehose/), which manages input and output files to be executed by GenePattern (Reich, M. et al. GenePattern 2.0. Nat. Genet. 38, 500-501 (2006)). Whole-exome sequencing BAM files for data from this study were deposited in dbGAP (phs()00488 for lung adenocarcinoma cases; phs000694 number pending for clinical cases).

[00314] Sequencing quality control. Quality control modules within Firehose were applied to all sequencing data for comparison of the origin for tumor and normal genotypes and to confinn fingerprinting concordance. Cross-contamination of samples was estimated using ContEst (Cibulskis, K. et al. Bioinformatics 27, 2601-2602 (2011)) to confirm that neither tumor nor germline sample had >3% contamination. Single nucleotide polymorphism fingerprints from each lane of a tumor and normal pair were cross-checked to confirm concordance, and nonmatching lanes were removed from analysis.

[0Θ315] Somatic alteration identification and annotation. The MuTect algorithm (Cibulskis, K. et al. Nat. Biotechnol. 31, 213-219 (2013)) was applied to identify somatic single- nucleotide variants in targeted exons. Indelocator

(ht^^A ^vAiroadinstitute.org^/cancer/cga/'indelocator/) was applied to identify small insertions or deletions. Annotation of identified variants was done using Oncotator (http://wv^.broadimtitute.org/cancer/cga/oncotator/). Rearrangements were identified using dRanger (http://www.broadiastitute.org/cancer/cga/brea^ointer ). Copy ratios were calculated for each hybrid capture bait by dividing the tumor coverage by the median coverage obtained in a set of reference normal samples (Chiang, D.Y. et al. Nat. Methods 6, 99-103 (2009)). The resulting copy ratios were segmented using the circular binary segmentation algorithm (Oishen, A.B., et al. Biostatistics 5, 557-572 (2004)). Genes in copy ratio regions with segment means of greater than 2 were evaluated for focal amplifications given the potential clinical significance of a large focal event. Genes in regions with segment means of less than -1 were evaluated for hemizygous or homozygous deletions, as either broad or focal deletions may involve genes with clinical relevance. RefSeq (Pruitt, K.D. et al. Nucleic Acids Res. 37, D32-D36 (2009)) was used to identify the genes that reside in the chromosomal coordinates demarcated by the segment start and end points.

[00316] Cross-validation of formalin-fixed, paraffin-embedded and fresh frozen mutation data. FFPE sections were received as 15-μηι slices (9 per sample), from 2007 to 2009. All FFPE samples were sequenced as described above with 100 ng of input DNA. Frozen tumor samples were sequenced according to established methods (Fisher, S. et al. Genome Biol. 12, Rl (2011)). All downstream computational analysis methods for assembly, alignment, mutation and copy number alteration identification were identical to the pipelines described above. For the downsampling experiment, MuTeet was rerun on all the cases with the 'downsample-to- coverage' parameter set to 90. Mutations in intronic regions were excluded. For cross-validation of mutations, validation power was defined as the probability to observe at least two alternative allele reads in the validation sample (given the allelic fraction, coverage in validation sample at that site and the assumption that the mutation should be present there).

[00317] Clinical gene database (TARGET). The TARGET (tumor alterations relevant for genomics-driven therapy) database included genes that, when altered somatically in cancers, met one of three criteria: (i) alterations in the gene predicted resistance and/or sensitivity to specific therapies, (ii) alterations in the gene had prognostic significance in a cancer type or (iii) alterations in the gene had diagnostic significance in a cancer type.

[00318] To build this database, Applicants performed a systematic review of the primary literature, manually curated specific genes based on clinician input and consulted expert opinion. This resulted in a list of 121 genes that met at least one of the three criteria required for entry into the TARGET database (Supplementary Table 5, available for download at htt : //www. bro adinstitute . or g/ c ancer/ c ga/^'tar get) .

[00319] Somatic heuristic algorithm for interpretation (PHIAL). Each somatic variant was scored individually using a series of rules and then was considered in aggregate to determine relationships between alterations in the same patient (for example, linked pathways). First, variants in TARGET are ranked highest, with scoring modifications for known mutational hotspots (for example, BRAF V600E), missense mutations in protein kinase regions and copy number alterations with directionality known to have clinical impact (for example, PTEN deletion). To assign maximum granularity between alterations, additional rules assign priority on the basis of presence of recurrent alterations in the Cancer Gene Census (Futreal, P. A. et al. Nat. Rev. Cancer 4, 177-183 (2004)), presence in the pathway of concurrently altered actionable genes in the same sample using curated cancer pathways from MSigDB (Subramanian, A. et al. Proc. Natl. Acad. Sci. USA 102, 15545-15550 (2005)), presence in known cancer pathways, gene sets or modules identified by MSigDB and finally presence in COSMIC (Forbes, S.A. et al. Nucleic Acids Res. 39, D945-D950 (2011)). All code for PHIAL was implemented using the R statistical package language and is available online

(http://w^w.broadinsti tute.org/cancer/cga/phial/).

[00320] Visual representation. A decision support tool built around the results was developed to allow curation team members and clinicians to engage the data with web-based resources integrated directly into the patient's results. The tool is built to convey effective clinical review with the minimum manual steps so that such a process can be scaled rapidly. The report structure was implemented using the Nozzle R package (Gehlenborg, N. et al. Bioinformatics 29, 1089-1091 (2013)). All clinically actionable relevant somatic variants were linked to search criteria in ClinicalTrials.gov.

[00321] Curation. Somatic alterations nominated by PHIA L, as 'investigate clinical relevance' were assigned for curation by a team of oncology and genomics experts charged with answering a series of structured questions pertaining to each nominated variant to facilitate final review (Fig. 11). A curated alteration required review of published data to determine which level of evidence could be assigned to a clinical action for the alteration.

[00322] Clinical trial data analyses. ClinicalTrials.gov (http://clinicaltrials.gov/) was accessed on 19 February 2013, and the search entry 'cancer' was used to extract all cancer- related clinical trials in the database. Duplicated trial entries and trials designated as 'Terminated' or 'Withdrawn' were excluded. Provided trial start-date dates (by year) were used to select all trials that were initiated between 2005 and 2012, and trial titles were queried using string matching in R for those that specifical ly mention TARGET genes in the title of the trial.

[00323] Ba/F3 experimental methods. Cell culture. HEK 293T cells were maintained in DMEM (Gibco) with 10% (vol/vol) FBS (Gibco). Ba/F3 cells (gift from A. Lane at Dana-Farber Cancer Institute) were maintained in RPMI 1640 (Gibco) with 10% FBS and 10 iig/mL mouse interleukin-3 (IL-3; Prospec). [00324] Retroviral injections. The wild-type JAK3 cDNA cloned in the pDONR223 vector was obtained from The Broad Institute RNAi Consortium. JAK3 mutations were generated by site-directed mutagenesis using the QuikCliange Lightning Mutagenesis Kit (Stratagene) and verified by full sequencing of the JAK3 cDNA insert. WT and mutant cDNAs were recombined into a Gateway adapted murine stem cell virus (MSCV)-puromycin vector (gift from A. Yoda at Dana Farber Cancer Institute) using the Gateway LR C!onase kit. Eco tropic viruses were produced by cotransfection of MSCV constructs with pCL-Eco vector (Imgenex) in HEK 293T cells. Ba/F3 cells were plated in 6-weil plates at a 30% con fluency and spin-infected at 800g for 90 min at 33 °C in the presence of 8 μ^'πιΕ polybrene (hexadimethrine bromide; Sigma). The same infection protocol was repeated 24 h later. Upon completion, the viral supernatant was removed and fresh medium added. Twenty-four hours after the medium change, Ba/F3 ceils were subjected to a 3-d puromyciii selection (2 fig/^'mL) in the presence of IL-3. Expression of ectopic JAK3 protein was verified by immunoblot analysis using a primar antibody against phospho-JAK3 (1 :500 dilution; Ceil Signaling #5031).

[00325] IL-3 Depletion. Ba./F3 cells and Ba,/F3 cells expressing WT and mutant forms of JAK3 were seeded in 25-cm^" vented-cap flasks at 20,000 ceils/mi in a total volume of 5 mi in the absence of IL-3 to select IL-3-independent cells. Cells were grown in the absence of IL-3 over several weeks. In parallel, Ba/F3 cells were maintained in 10 ng ml IL-3 throughout as a positive control Cell counts were recorded every 4 d using ViCell counter and split as needed.

[00326] Statistical analyses. Statistical analysis of raw sequencing metrics. All analyses of raw sequencing metrics were performed using the R statistical package. Sample size was established by incorporating all available FFPE samples sequenced under the FFPE sequencing protocol by the time of analysis freeze (n = 99). Significance between two means (FFPE and non-FFPE samples for the sequencing metrics) was calculated with the two-tailed Mann- Whitney C/-test, given the non-normal distribution of values. P < 0.05 was considered significant.

[00327] Statistical analysis of formalin-fixed, paraffin-embedded and frozen tissue. Two- tailed Fisher's exact test was used to test the statistical significance of the contingency table represented by tissue type (FFPE or frozen) and validation status, Pearson's correlation was performed on log₂ (target copy ratio) segment mean data for FFPE and frozen exon targets, and significance was calculated using Pearson's product moment correlation coefficient. Sample size for exons from all 1 1 cases (n ^:::: 1 ,338,859) greatly exceeded the minimum sample size needed to determine a linear correlation coefficient of 0.8 with power of 0.8 and significance level of 0.05. The variance estimate among FFPE (0.054) and frozen (0.049) copy number signal data was similar. Whole-exome sequencing data for lung adenocarcinoma cases were deposited in dbGaP (phs000488).

* * *

[00328] While preferred embodiments of the present invention have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the invention. It should be understood that various aiternatives to the embodiments of the invention descri bed herein may be employed in practicing the invention.

Claims

What is claimed is:

1 , A method of evaluating and ranking genomic alterations in tumor tissue comprising identifying somatic gene variants having clinical or biological relevance for personalized patient tumor treatment options for treating a patient in need of tumor treatment,

comprising the steps of:

(a) as to tumor tissue of the patient ("patient tumor tissue") that has been subjected to whole exome-sequencing and archival tumor tissue samples that have been subjected to whole-exome sequencing (i) determining concordance of mutations observed in patient tumor tissue that are observed in archival tumor samples and (ii) determining concordance of mutations observed in archival tumor samples that are observed in patient tumor tissue, whereby somatic variants are obtained;

(b) generating or accessing a database of genes having therapeutic, prognostic or diagnostic implications for cancer patients or patients having tumors;

(c) sorting each somatic variant obtained in step (a) by clinical and biological relevance;

(d) linking genes from the database generated or accessed in step (b) with additional biological significant gene data; and

(e) demoting vari ants of uncertain significance, or promoting certain variants of significance; whereby variants of significance are identified and somatic gene alterations having clinical or biological relevance are identified for personalized patient treatment options.

2, A method of evaluating and ranking genomic alterations in tumor tissue comprising identifying somatic gene variants having clinical or biological relevance for personalized patient tumor treatment options for treating a patient in need of tumor treatment,

comprising the steps of:

(a) performing whole-exome sequencing on tumor tissue of the patient ("patient tumor tissue");

(b) performing whole-exome sequencing on archival tumor tissue samples;

(c) (i) determining concordance of mutations observed in patient tumor tissue that are observed in archival tumor samples and (ii) determining concordance of mutations observed in archival tumor samples that are observed in patient tumor tissue, whereby somatic variants are obtained; (d) generating or accessing a database of genes having therapeutic, prognostic or diagnostic implications for cancer patients;

(e) sorting each somatic variant obtained in step (c) by clinical and biological relevance;

(f) linking genes from the database generated or accessed in step (d) with additional biological significant gene data; and

(g) demoting variants of uncertain significance, or promoting certain variants of significance; whereby variants of significance are identified and somatic gene alterations having clinical or biological relevance are identified for personalized patient treatment options.

3. The method of claim 1 or 2 wherein the whoie-exome sequencing comprises whole-exome sequencing on formalin- fixed paraffin embedded (FFPE) patient tumor tissue.

4. The method of claim 1 or 2, wherein the tumor comprises gastrointestinal stromal tumors, or skin, for example squamous cell carcinoma; a hematopoieitic tumor of lymphoid lineage, for example leukemia, acute lymphocytic leukemia, chronic lymphocytic leukemia, B-cell lymphoma (such as diffuse large B ceil lymphoma), T-cell lymphoma, Hodgkin's lymphoma, non-Hodgkin's lymphoma, hairy cell lymphoma, or Burkitt's lymphoma; a hematopoieitic tumor of myeloid lineage, including, but not limited to acute myeloid leukemia, chronic myeloid leukemias, myelogenous leukemias, and Imatinib sensitive and refractory chronic myelogenous leukemias, myelodysplastic syndrome, Bortezomib sensitive and refractory multiple myeloma, myeloproliferative disease or promyelocytic leukaemia; thyroid follicular cancer; a tumor of mesenchymal origin, for example fibrosarcoma or rhabdomyosarcoma; a tumour of the central or peripheral nervous system, for example astrocytoma, neuroblastoma, glioma (a High grade glioma) or schwannoma; melanoma (e.g. malignant or metastatic melanoma); seminoma;

teratocarcinoma; osteosarcoma; keratoacanthoma; thyroid follicular cancer; Kaposi's sarcoma or Swing's sarcoma.

5. The method of claim 1 or 2 wherein the demoting is based on scoring modifications for known mutations, missense mutations in protein kinase regions, cop)' number alterations with directionality known to have clinical impact, presence of recurrent alterations in a known database, presence in the pathway of concurrently altered actionable genes in the same sample using curated cancer pathways from a known database, or presence in known cancer pathways, gene sets, or modules identified in a known database

6. The method of claim 1 or 2 wherein the promoting is based on scoring modifications for known mutations, missense mutations in protein kinase regions, copy number alterations with directionality known to have clinical impact, presence of recurrent alterations in a known database, presence in the pathway of concurrently altered actionable genes in the same sample using curated cancer pathways from a known database, or presence in known cancer pathways, gene sets, or modules identified in a known database.