WO2023056451A1

WO2023056451A1 - Compositions and methods for assaying for and genotyping genetic variations

Info

Publication number: WO2023056451A1
Application number: PCT/US2022/077396
Authority: WO
Inventors: James Paul BROUGHTON; Janice Sha CHEN; Sophia HUBBELL
Original assignee: Mammoth Biosciences, Inc.
Priority date: 2021-09-30
Filing date: 2022-09-30
Publication date: 2023-04-06

Abstract

Described herein are compositions of RNA and effector protein components for use in methods of target nucleic acid detection and genotyping. Also described herein, are methods of assaying for a target nucleic acid comprising a nucleotide variant at a position of interest. Also described herein are methods of determining a variant genotype in an organism.

Description

COMPOSITIONS AND METHODS FOR ASSAYING FOR AND GENOTYPING GENETIC VARIATIONS CROSS-REFERENCE [0001] This application claims priority to U.S. Provisional Application Serial No. 63/250,991, filed on September 30, 2021, which is incorporated herein by reference in its entirety for all purposes. BACKGROUND [0002] There is a long-standing need in the life sciences for identifying and genotyping mutations rapidly, accurately, and cost-effectively. Detection of small genetic variations that can lead to major changes in phenotype, including both physical differences that make us unique and pathological changes underlying disease, can provide guidance on treatment or intervention to reduce the progression of ailments, as well as improve understanding of gene and protein function that can have wide-ranging applications. Genetic variation among humans can be used to identify disease-causing genes in humans and to explain and diagnose many diseases. For example, single nucleotide polymorphisms (SNPs) are the most common type of genetic variation among humans and can be used to identify multiple human diseases. Small insertions and deletions, transversions and duplications are other common mutations in the human genome, also known to have a significant influence on genetic variation and human disease. Accordingly, there exists a need for improved genotyping systems and methods to detect and genotype target nucleic acids comprising genetic variations, including somatic mutations, polymorphisms, and other mutations indicative of disease states. Genotyping organisms also has implications beyond disease diagnosis, such as breeding livestock, crop management, and improving our understanding of complex phenotypic relationships. SUMMARY [0003] Provided herein, in certain embodiments, is a method of assaying for a target nucleic acid comprising a nucleotide variant at a position of interest, the method comprising: contacting a sample to: a composition comprising an effector protein and a guide nucleic acid; and, a reporter, and detecting a presence or absence of a target nucleic acid comprising the nucleotide variant in the sample by assaying for a signal indicative of cleavage of the reporter by the effector protein; and comparing the signal to a control signal produced by contacting the composition and reporter to a control nucleic acid molecule not comprising the nucleotide variant, but that is otherwise at least 90% identical to the target nucleic acid, e.g., at least apart from a variation of less than twenty nucleotides. In some embodiments, assaying for a signal produced by the effector protein comprises assaying for a signal, or change in signal, produced by trans cleavage of the reporter by the effector protein, wherein the trans cleavage is activated upon hybridization of the guide nucleic acid to the target nucleic acid molecule comprising the nucleotide variant. In some embodiments, the control nucleic acid molecule is otherwise identical to the target nucleic acid molecule, apart from a variation of less than four nucleotides. In some embodiments, the control nucleic acid molecule varies from the target nucleic acid molecule by no more than two nucleotides. In some embodiments, the control nucleic acid molecule is otherwise identical to the target nucleic acid molecule. In some embodiments, the nucleotide variant is a point mutation in the target nucleic acid molecule, relative to an otherwise identical target nucleic acid molecule. In some embodiments, the nucleotide variant is a non- synonymous mutation. In some embodiments, the nucleotide variant is a point mutation, an insertion, a deletion, a duplication, a transversion, or a combination thereof. In some embodiments, the nucleotide variant is a somatic mutation. In some embodiments, the nucleotide variant is a synonymous mutation. In some embodiments, the nucleotide variant is a missense mutation, a nonsense mutation, or a non-stop mutation. In some embodiments, the point mutation is a single nucleotide polymorphism (“SNP”). In some embodiments, the nucleotide variant is disease-causing, at least in part, or is associated with a disease. In some embodiments, the disease is a cancer, an inherited disorder, an ophthalmological disorder, an endocrinological disorder, an autoimmune disorder, a metabolic disorder, or a combination thereof. In some embodiments, the metabolic disorder is nonalcoholic fatty liver disease, alcoholic liver disease, liver disease, hepatitis, chronic hepatitis, hepatocellular carcinoma, diabetes, cirrhosis, steatosis, fibrosis, obesity, or a combination thereof. In some embodiments, the metabolic disorder is liver disease. In some embodiments, the disease is selected from a group consisting of: asthma, arrhythmia, blood pressure, biliary cirrhosis, bipolar affective disorder, colorectal cancer, Crohn’s Disease, dyslipidemia, eating disorder, esophageal adenocarcinoma, hyperbilirubinemia, idiopathic arthritis, idiopathic PD and FTD, knee and hip osteoarthritis, lung cancer, myocardial infraction, migraine, obesity, ossification, oxalate stone, POAG, rheumatoid arthritis, systemic sclerosis, severe sepsis, Type II diabetes, ulcerative colitis, urinary bladder cancer, and autism. [0004] In some embodiments, the target nucleic acid is, or is encoded by, a gene selected from a group consisting of: EDN1, NOS1, KCN1, TAF1, MBL, HRT 3A, Cyclin D1, UGT1A1 UDP, MIF, SNCA, LRRK2, MMP1, PAI, PAI1, Npps, CDH, CDH1, POAG, TNF, TNF-α, MDR1, TSP, PCS, PNPLA3, IR, INSR, CNP, LPL, MCR, MC1R, TMEM, C9ORF72, MAPT, GRN, COL, p53, MYOC, FBN1, STX1A, CCN, CCND1 cyclin D1, a fragment thereof, or any combination thereof. In some embodiments, the target nucleic acid is, or is encoded by, a PNPLA3 gene or a fragment thereof. In some embodiments, the target nucleic acid is a fragment of a PNPLA3 gene. In some embodiments, the PNPLA3 gene comprises a substitution of a C with a G at nucleotide position 444 of a wild-type PNPLA3 gene. In some embodiments, the PNPLA3 gene encodes a PNPLA3 protein comprising an I to M substitution at amino acid position of 148 of a wild-type PNPLA3 protein. In some embodiments, the nucleotide variant is an SNP, a marker of a disease, or a combination thereof. In some embodiments, the method comprises determining whether an organism from which the sample is derived is homozygous for the nucleotide variant. In some embodiments, the method comprises determining whether an organism from which the sample is derived is heterozygous for the nucleotide variant. In some embodiments, the effector protein is a Type V or Type VI Cas effector protein. In some embodiments, the type V Cas effector protein is a Cas12 protein. In some embodiments, the Cas12 protein comprises a Cas12a polypeptide, a Cas12b polypeptide, a Cas12c polypeptide, a Cas12d polypeptide, a Cas12e polypeptide, a C2c4 polypeptide, a C2c8 polypeptide, a C2c5 polypeptide, a C2c10 polypeptide, or a C2c9 polypeptide. In some embodiments, the Cas12 protein is at least 80% identical to SEQ ID NO: 11. In some embodiments, the Cas12 protein is at least 95% identical to SEQ ID NO: 11. In some embodiments, the Cas12 protein is SEQ ID NO: 11. In some embodiments, the type V Cas effector protein is a Cas14 protein. In some embodiments, the Cas14 protein comprises a Cas14a polypeptide, a Cas14b polypeptide, a Cas14c polypeptide, a Cas14d polypeptide, a Cas14e polypeptide, a Cas14f polypeptide, a Cas14g polypeptide, a Cas14h polypeptide, a Cas14i polypeptide, a Cas14j polypeptide, or a Cas14k polypeptide. In some embodiments, the type V Cas effector protein is a CasФ protein. In some embodiments, the type VI Cas effector protein is a Cas13 protein. In some embodiments, the Cas13 protein comprises a Cas13a polypeptide, a Cas13b polypeptide, a Cas13c polypeptide, a Cas13c polypeptide, a Cas13d polypeptide, or a Cas13e polypeptide. In some embodiments, the reporter comprises a fluorophore, a quencher, or a combination thereof. In some embodiments, the reporter comprises a fluorescence resonance energy transfer (FRET) pair. In some embodiments, the target nucleic acid is DNA. In some embodiments, the DNA is single or double stranded DNA. In some embodiments, the DNA is purified genomic DNA. In some embodiments, the DNA is pre-amplified DNA. In some embodiments, the target nucleic acid is RNA. In some embodiments, the RNA is double stranded or single stranded RNA. In some embodiments, the RNA is purified genomic RNA. In some embodiments, the RNA is pre- amplified RNA. In some embodiments, the sample is suspended in a buffer composition. In some embodiments, the sample is suspended in a buffer composition with a pH of about 7 to about 9. In some embodiments, the sample is suspended in a buffer composition that enhances DNA detection. In some embodiments, the sample comprises at most 250 target nucleic acid copies per assay. In some embodiments, the sample is derived from an organism selected from the group consisting of: unicellular organisms, multicellular organisms, pathogenic organisms, living organisms, or any combination thereof. In some embodiments, the living organism is a human, an animal, a plant, a crop, or any combination thereof. In some embodiments, the Cas12 protein associates with a gRNA comprising a nucleotide sequence that is at least 75% identical to any one of SEQ ID NOs: 209-366. In some embodiments, the Cas12 protein associates with a gRNA comprising a nucleotide sequence that is at least 95% identical to any one of SEQ ID NOs: 209- 366. In some embodiments, the Cas12 protein associates with a gRNA comprising a nucleotide sequence that is at least 100% identical to any one of SEQ ID NOs: 209-366. [0005] Also provided herein, in certain embodiments, is a method for determining a variant genotype in an organism, comprising: assaying for at least one target nucleic acid comprising a genomic variant in a sample by assaying for a first signal indicative of activity of a first effector protein; assaying for at least one target nucleic acid not comprising the genomic variant in the sample by assaying for a second signal indicative of activity of a second effector protein; and comparing the first signal and the second signal. In some embodiments, assaying for at least one target nucleic acid comprising the genomic variant comprises: (i) contacting at least a first portion of the sample to a first composition comprising a first effector protein, a first guide nucleic acid, and a first reporter; and (ii) detecting the presence or absence of a target nucleic acid comprising the genomic variant by assaying for a first signal, or change in first signal, produced by trans cleavage of the first reporter by the first effector protein, wherein the trans cleavage is activated upon hybridization of the first guide nucleic acid to the target nucleic acid molecule comprising the genomic variant. In some embodiments, assaying for at least one target nucleic acid not comprising the genomic variant comprises: (i) contacting at least a second portion of the sample to: a second composition comprising a second effector protein, a second guide nucleic acid, and a second reporter; and (ii) detecting the presence or absence of a target nucleic acid not comprising the genomic variant by assaying for a second signal, or change second in signal, produced by trans cleavage of the second reporter by the second effector protein, wherein the trans cleavage is activated upon hybridization of the second guide nucleic acid to the target nucleic acid molecule not comprising the genomic variant. In some embodiments, the genomic variant is an SNP. In some embodiments, the genomic variant is a somatic mutation. In some embodiments, the method comprises determining whether the organism is homozygous or heterozygous for the genomic variant. In some embodiments, the method further comprises determining whether the organism is homozygous or heterozygous for the genomic variant comprises comparing the level of the first detectable signal to the level of the second detectable signal. In some embodiments the method further comprises identifying the organism as heterozygous for the genomic variant if the level of the first detectable signal is about equal to the level of the second detectable signal. In some embodiments, the method further comprises identifying the organism as homozygous for the genomic variant if the level of the first detectable signal is higher than the level of the second detectable signal. In some embodiments, the method further comprises identifying the organism as homozygous for a wild- type if the level of the second detectable signal is higher than the level of the first detectable signal. In some embodiments, the first reporter nucleic acid, the second reporter nucleic acid, or a combination thereof, comprise a fluorophore, a quencher, or a combination thereof. In some embodiments, the first reporter nucleic acid, the second reporter nucleic acid, or a combination thereof, comprise a fluorescence resonance energy transfer (FRET) pair. In some embodiments, the target nucleic acids are DNA. In some embodiments, the DNA is single or double stranded DNA. In some embodiments, the DNA is purified genomic DNA. In some embodiments, the DNA is pre-amplified DNA. In some embodiments, the target nucleic acids are RNA. In some embodiments, the RNA is double stranded or single stranded RNA. In some embodiments, the RNA is purified genomic RNA. In some embodiments, the RNA is pre-amplified RNA. In some embodiments, the organism is selected from a group consisting of: unicellular organisms, multicellular organisms, pathogenic organisms, living organisms, or any combination thereof. In some embodiments, the living organism is a human, an animal, a plant, a crop, or any combination thereof. In some embodiments, the assaying for the target nucleic acid comprising the genomic variant and the assaying for the target nucleic acid not comprising the genomic variant, are performed in a single reaction, in a single volume, or a combination thereof. In some embodiments, the first signal, the second signal, or a combination thereof, is detected at least at one point in time. In some embodiments, the reaction time for detecting the first signal, the second signal, or a combination thereof, is less than about 10 minutes. In some embodiments, the reaction time for detecting the first signal, the second signal, or a combination thereof, is less than about 15 minutes. In some embodiments, the reaction time for detecting the first signal, the second signal, or a combination thereof, is from about 10 minutes to about 30 minutes. In some embodiments, the method further comprises amplifying the target nucleic acid comprising the genomic variant, the target nucleic acid not comprising the genomic variant, or a combination thereof. In some embodiments, the amplifying comprises: transcription mediated amplification (TMA), helicase dependent amplification (HDA), or circular helicase dependent amplification (cHDA), strand displacement amplification (SDA), recombinase polymerase amplification (RPA), loop mediated amplification (LAMP), exponential amplification reaction (EXPAR), rolling circle amplification (RCA), ligase chain reaction (LCR), simple method amplifying RNA targets (SMART), single primer isothermal amplification (SPIA), multiple displacement amplification (MDA), nucleic acid sequence based amplification (NASBA), hinge-initiated primer-dependent amplification of nucleic acids (HIP), nicking enzyme amplification reaction (NEAR), and improved multiple displacement amplification (IMDA), or any combination thereof. In some embodiments, the amplification reaction time is from about 10 minutes to about 30 minutes. In some embodiments, the amplification reaction time is less than about 20 minutes. In some embodiments, the assaying is carried out in vitro. In some embodiments, the first effector protein, the second effector protein, or a combination thereof, is a Type V or Type VI Cas effector protein. In some embodiments, the type V Cas effector protein is a Cas12 protein. In some embodiments, the Cas12 protein comprises a Cas12a polypeptide, a Cas12b polypeptide, a Cas12c polypeptide, a Cas12d polypeptide, a Cas12e polypeptide, a C2c4 polypeptide, a C2c8 polypeptide, a C2c5 polypeptide, a C2c10 polypeptide, or a C2c9 polypeptide. In some embodiments, the Cas12 protein is at least 80% identical to SEQ ID NO: 11. In some embodiments, the Cas12 protein is at least 95% identical to SEQ ID NO: 11. In some embodiments, the Cas12 protein is SEQ ID NO: 11. In some embodiments, the type V Cas effector protein is a Cas14 protein. In some embodiments, the Cas14 protein comprises a Cas14a polypeptide, a Cas14b polypeptide, a Cas14c polypeptide, a Cas14d polypeptide, a Cas14e polypeptide, a Cas14f polypeptide, a Cas14g polypeptide, a Cas14h polypeptide, a Cas14i polypeptide, a Cas14j polypeptide, or a Cas14k polypeptide. In some embodiments, the type V Cas effector protein is a CasФ protein. In some embodiments, the type VI Cas effector protein is a Cas13 protein. In some embodiments, the Cas13 protein comprises a Cas13a polypeptide, a Cas13b polypeptide, a Cas13c polypeptide, a Cas13c polypeptide, a Cas13d polypeptide, or a Cas13e polypeptide. In some embodiments, the sample is suspended in a buffer composition. In some embodiments, the sample is suspended in a buffer composition with a pH of about 7 to about 9. In some embodiments, the sample is suspended in a buffer composition that enhances DNA detection. In some embodiments, the sample comprises at most 250 target nucleic acid copies per assay. In some embodiments, the SNP is disease-causing, at least in part, or is associated with a disease. In some embodiments, the disease a cancer, an inherited disorder, an ophthalmological disorder, or a combination thereof. In some embodiments, the disease is cancer, an endocrinological disorder, an autoimmune disorder, or a metabolic disorder. In some embodiments, the metabolic disorder is nonalcoholic fatty liver disease, alcoholic liver disease, liver disease, hepatitis, chronic hepatitis, hepatocellular carcinoma, diabetes, cirrhosis, steatosis, fibrosis, or obesity. In some embodiments, the metabolic disorder is liver disease. In some embodiments, the SNP is associated with a disease selected from a group consisting of: asthma, arrhythmia, blood pressure, biliary cirrhosis, bipolar affective disorder, colorectal cancer, Crohn’s Disease, dyslipidemia, eating disorder, esophageal adenocarcinoma, hyperbilirubinemia, idiopathic arthritis, idiopathic PD and FTD, knee and hip osteoarthritis, lung cancer, myocardial infraction, migraine, obesity, ossification, oxalate stone, POAG, rheumatoid arthritis, systemic sclerosis, severe sepsis, Type II diabetes, ulcerative colitis, urinary bladder cancer, and autism. In some embodiments, the target nucleic acid comprising the SNP, the target nucleic acid not comprising the SNP, or a combination thereof, is, or is encoded by, a gene selected from a group consisting of: EDN1, NOS1, KCN1, TAF1, MBL, HRT 3A, Cyclin D1, UGT1A1 UDP, MIF, SNCA, LRRK2, MMP1, PAI, PAI1, Npps, CDH, CDH1, POAG, TNF, TNF-α, MDR1, TSP, PCS, PNPLA3, IR, INSR, CNP, LPL, MCR, MC1R, TMEM, C9ORF72, MAPT, GRN, COL, p53, MYOC, FBN1, STX1A, CCN, CCND1 cyclin D1, a fragment thereof, or any combination thereof. In some embodiments, the target nucleic acid comprising the genomic variant, the target nucleic acid not comprising the genomic variant, or a combination thereof, is, or is encoded by, a PNPLA3 gene, or a fragment thereof. In some embodiments, the target nucleic acid comprising the genomic variant is a PNPLA3 gene comprising a substitution of a C with a G at nucleotide position 444 of a wild-type PNPLA3 gene, or a fragment thereof. In some embodiments, the PNPLA3 gene encodes a PNPLA3 protein comprising an I to M substitution at amino acid position of 148 of a wild-type PNPLA3 protein. In some embodiments, the target nucleic acid not comprising the genomic variant is a wild-type PNPLA3 gene, or a fragment thereof. In some embodiments, the target nucleic acid not comprising the genomic variant is a PNPLA3 gene comprising a substitution at nucleotide position 443 of a wild-type PNPLA3 gene, or a fragment thereof. In some embodiments, the Cas12 protein associates with a gRNA comprising a nucleotide sequence that is at least 75% identical to any one of SEQ ID NOs: 209-366. In some embodiments, the Cas12 protein associates with a gRNA comprising a nucleotide sequence that is at least 95% identical to any one of SEQ ID NOs: 209-366. In some embodiments, the Cas12 protein associates with a gRNA comprising a nucleotide sequence that is at least 100% identical to any one of SEQ ID NOs: 209-366. BRIEF DESCRIPTION OF THE DRAWINGS [0006] The novel features of the disclosure are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present disclosure will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the disclosure are utilized, and the accompanying drawings of which: [0007] FIG.1 depicts a schematic diagram of a workflow for assaying purified genomic DNA for a target nucleic acid molecule comprising a nucleotide variant at a position of interest, according to at least some embodiments disclosed herein. [0008] FIG.2 depicts a schematic diagram of a workflow for assaying DNA sample for a target nucleic acid molecule comprising a nucleotide variant at a position of interest, according to at least some embodiments disclosed herein. [0009] FIG.3 depicts assaying samples containing synthetic control nucleic acids in different crude lysis buffers, according to at least some embodiments disclosed herein. [0010] FIG.4 depicts a graph showing the results of a 30 minute fluorescent amplification reaction of crude samples in varying reaction conditions and using different reagent mixtures. [0011] FIGS.5A-5B depicts a graph showcasing detection of samples containing synthetic control nucleic acids assayed to determine a baseline fluorescence for each PNPLA3 genotype. Samples were either homozygous for the wild type allele (“wild-type control”), heterozygous for the wild type allele and the at-risk allele (“het control”), homozygous for the at- risk allele (“mutant control”), or contained no target (“NTC”). FIG.5A shows samples target amplified with loop-mediated isothermal amplification (LAMP), as measured in raw florescence (au), according to at least some embodiments disclosed herein. FIG.5B shows DETECTR assay measuring synthetic control samples for different genetic combinations of PNPLA3 alleles, as measured in raw florescence (au), according to at least some embodiments disclosed herein. [0012] FIG.6 depicts a graph showcasing DETECTR target data from synthetic control nucleic acid sample, as measured in ratio of normalized florescence (au), calculated to distinguish between wild type, heterozygous, and homozygous target sequences, according to at least some embodiments disclosed herein. [0013] FIG.7 depicts a graph showcasing PNPLA3 DETECTR genotyping data from pre-amplified clinical sample showing differentiation as wild-type, heterozygous, and homozygous as measured in florescence signal ratio, according to at least some embodiments disclosed herein. [0014] FIGS.8A-8B depicts graphs showing the results of the PNPLA3 DETECTR reaction, as measured in raw fluorescence, performed on ten different blinded clinical samples. FIG.8A shows the ten samples target amplified with loop-mediated isothermal amplification (LAMP), as measured in raw florescence. FIG.8B shows DETECTR assay measuring the samples for different genetic combinations of PNPLA3 alleles, as measured in raw florescence. [0015] FIG.9 depicts a graph showing a re-run of the PNPLA3 DETECTR reaction on select clinical samples, from the group of 10 clinical samples referenced in FIGS.7 and 8. [0016] FIG.10 depicts gel electrophoresis for DNAs extracted from samples 127-1453, 127-1452, and 127-1447, referenced in FIGS.7-9, and amplified by PNPLA3 specific PCR. 127-1453 failed to amplify by PCR, which suggests that there might have been very little genetic material on the sample swab. [0017] FIG.11 depicts a graph showing a re-run of the PNPLA3 DETECTR reaction on select clinical samples, from the group of 10 clinical samples referenced in FIGS.7 and 8 with a 30 minute detection reaction time. [0018] FIG.12 depicts a graph showing a re-run of the PNPLA3 DETECTR reaction on select clinical samples, from the group of 10 clinical samples referenced in FIGS.7 and 8 to examiner variability among multiple replicate runs. [0019] FIG.13 depicts a table showcasing PNPLA3 DETECTR genotyping results for three replicates per clinical sample, differentiated as wild-type, heterozygous, and homozygous, according to at least some embodiments disclosed herein. DETAILED DESCRIPTION [0020] It is to be understood that both the foregoing general description and the following detailed description are exemplary and explanatory only and are not restrictive of the disclosure. [0021] The section headings used herein are for organizational purposes only and are not to be construed as limiting the subject matter described. All documents, or portions of documents, cited in this application, including, but not limited to, patents, patent applications, articles, books, and treatises, are hereby expressly incorporated by reference in their entirety for any purpose. Definitions [0022] Unless the context requires otherwise, throughout the specification and claims which follow, the word “comprise” and variations thereof, such as, “comprises” and “comprising” are to be construed in an open, inclusive sense, that is, as “including, but not limited to.” As used in this specification and the appended claims, the singular forms “a,” “an,” and “the” include plural referents unless the content clearly dictates otherwise. It should also be noted that the term “or” is generally employed in its sense including “and/or” unless the content clearly dictates otherwise. As used herein, the term “and/or” includes any and all combinations of one or more of the associated listed items. [0023] As used herein, the term “about” in reference to a number or range of numbers is understood to mean the stated number and numbers +/- 10% thereof, or 10% below the lower listed limit and 10% above the higher listed limit for the values listed for a range. The term “about” also includes an amount that would be expected to be within experimental error. The term “about” also includes the exact amount. [0024] “Consisting essentially of,” when used to define compositions and methods, shall mean excluding other elements of any essential significance to the combination for the stated purpose. Thus, a composition consisting essentially of the elements as defined herein would not exclude other materials or steps that do not materially affect the basic and novel characteristic(s) of the claimed invention. “Consisting of” shall mean excluding more than trace elements of other ingredients and substantial method steps. Embodiments defined by each of these transition terms are within the scope of this disclosure. [0025] As used herein, the term “comprising” and its grammatical equivalents specifies the presence of stated features, integers, steps, operations, elements, and/or components, but do not preclude the presence or addition of one or more other features, integers, steps, operations, elements, components, and/or groups thereof. [0026] As used herein, the terms “individual,” “subject,” and “patient” are used interchangeably and include any member of the animal kingdom, including humans. None of the terms require or are limited to situations characterized by the supervision (e.g. constant or intermittent) of a health care worker (e.g. a doctor, a registered nurse, a nurse practitioner, a physician’s assistant, an orderly or a hospice worker). [0027] As used herein, the terms “percent identity” and “% identity” refer to the extent to which two sequences (nucleotide or amino acid) have the same residue at the same positions in an alignment. For example, “an amino acid sequence is X% identical to SEQ ID NO: Y” refers to % identity of the amino acid sequence to SEQ ID NO: Y and is elaborated as X% of residues in the amino acid sequence are identical to the residues of sequence disclosed in SEQ ID NO: Y. Generally, computer programs may be employed for such calculations. Illustrative programs that compare and align pairs of sequences, include ALIGN (Myers and Miller, Comput Appl Biosci. 1988 Mar;4(1):11-7), FASTA (Pearson and Lipman, Proc Natl Acad Sci U S A.1988 Apr;85(8):2444-8; Pearson, Methods Enzymol.1990;183:63-98) and gapped BLAST (Altschul et al., Nucleic Acids Res.1997 Sep 1;25(17):3389-40), BLASTP, BLASTN, or GCG (Devereux et al., Nucleic Acids Res.1984 Jan 11;12(1 Pt 1):387-95). [0028] The term, “complementary,” as used herein with reference to a nucleic acid refers to the characteristic of a polynucleotide having nucleotides that base pair with their Watson- Crick counterparts (C with G; or A with T/U) in a reference nucleic acid. For example, when every nucleotide in a polynucleotide forms a base pair with a reference nucleic acid, that polynucleotide is said to be 100% complementary to the reference nucleic acid. In a double stranded DNA or RNA sequence, the upper (sense) strand sequence is in general, understood as going in the direction from its 5′- to 3′-end, and the complementary sequence is thus understood as the sequence of the lower (antisense) strand in the same direction as the upper strand. Following the same logic, the reverse sequence is understood as the sequence of the upper strand in the direction from its 3′- to its 5′-end, while the ‘reverse complement’ sequence or the ‘reverse complementary’ sequence is understood as the sequence of the lower strand in the direction of its 5′- to its 3′-end. Each nucleotide in a double stranded DNA or RNA molecule that is paired with its Watson-Crick counterpart called its complementary nucleotide. [0029] The terms, “non-naturally occurring” and “engineered,” as used herein are used interchangeably and indicate the involvement of human intervention. The terms, when referring to a nucleic acid, nucleotide, protein, polypeptide, peptide or amino acid, refer to a nucleic acid, nucleotide, protein, polypeptide, peptide or amino acid that is at least substantially free from at least one other feature with which it is naturally associated in nature and as found in nature, and/or contains a modification (e.g., chemical modification, nucleotide sequence, or amino acid sequence) that is not present in the naturally occurring nucleic acid, nucleotide, protein, polypeptide, peptide, or amino acid. The terms, when referring to a composition or system described herein, refer to a composition or system having at least one component that is not naturally associated with the other components of the composition or system. By way of a non- limiting example, a composition may include an effector protein and a guide nucleic acid that do not naturally occur together. Conversely, and as a non-limiting further clarifying example, an effector protein or guide nucleic acid that is “natural,” “naturally-occurring,” or “found in nature” includes an effector protein and a guide nucleic acid from a cell or organism that have not been genetically modified by human intervention. [0030] The term, “target nucleic acid,” as used herein refers to a nucleic acid that is selected as the nucleic acid for modification, binding, hybridization or any other activity of or interaction with a nucleic acid, protein, polypeptide, or peptide described herein. A target nucleic acid may comprise RNA, DNA, or a combination thereof. A target nucleic acid may be single- stranded (e.g., single-stranded RNA or single-stranded DNA) or double-stranded (e.g., double- stranded DNA). [0031] The term, “target sequence,” as used herein when used in reference to a target nucleic acid refers to a sequence of nucleotides that hybridizes to a portion (preferably an equal length portion) of a guide nucleic acid. Hybridization of the guide nucleic acid to the target sequence may bring an effector protein into contact with the target nucleic acid. [0032] As used herein, the term “organism,” refers to any of unicellular organisms, multicellular organisms, pathogenic organisms (e.g., virus, bacterium, fungi, protozoa, worm, or other agent(s) or organism(s) responsible for and/or related to a disease or condition in living organisms), and living organisms (e.g., humans, animals, plants, crops, and the like). [0033] As used herein, the term “single nucleotide polymorphism” or “SNP,” refers to the variation of a single nucleotide or nucleotide at a specific position in a nucleic acid sequence. The single nucleotide or nucleotide variation is generally between the genomes of two members of the same species, or some other specific population. In some cases, a SNP occurs at a specific nucleic acid site in genomic DNA in which different alternative sequences, e.g., “alleles,” exist more frequently in certain member of a population. In some cases, a less frequent allele comprises the SNP and has an abundance of at least 1%, 0.8%, 0.5%, 0.4%, 0.3%, 0.2% or 0.1%. In some instances, a SNP is any point mutation that is sufficiently present in a population (e.g., 1%, 0.8%, 0.5%, 0.4%, 0.3%, 0.2%, 0.1% or more). A SNP may be disease-causing, at least partially, or may be associated with a disease. SNPs are known to skilled artisans and can be located in relevant published papers and genomic databases. [0034] As used herein, the term “somatic mutation,” refers to any alteration in the DNA of a somatic cell of an organism. Somatic mutations can occur in any of the cells of the body except the germ cells (sperm and egg) and therefore are not passed on to children. These alterations can (but do not always) cause cancer or other diseases. [0035] As used herein, the term “allele” refers to a variant of a given gene and can be the result of a SNP or any sequence variation from a reference sequence. From any number of different alleles of a given gene, an allelic frequency can be determined, thereby providing the fraction of all chromosomes that carry a particular allele of a gene within a specific population. [0036] As used herein, the term “wild-type,” or “wild-type variant” refers to a segment or region of nucleic acid sequence, or fragment thereof, that is the universal form (e.g., present in at least 40%) within a population. In some embodiments, “wild-type,” or “wild-type variant” refers to a segment or region of nucleic acid sequence, or fragment thereof, lacking commonly known sequence variations or allelic variations which may be silent, causal, disease-associated, or disease-risk causing. In some embodiments, “wild-type,” or “wild-type variant” refers to a to a polypeptide or protein expressed by a naturally occurring organism, or a polypeptide or protein having the characteristics of a polypeptide or protein isolated from a naturally occurring organism, wherein the polypeptide or protein is relatively constant (e.g., present in at least 40% of) a species population. [0037] As used herein, the term “CRISPR effector,” “effector,” “CRISPR-associated protein,” “Cas effector,” “Cas protein,” or “CRISPR enzyme,” refers a polypeptide, or a fragment thereof, possessing enzymatic activity, and that is capable of binding to a target nucleic acid molecule with the support of a guide nucleic acid molecule. In some embodiments, the binding is sequence-specific. In some embodiments, the guide nucleic acid molecule is DNA or RNA. In different embodiments, the target nucleic acid molecule may be DNA or RNA. In some embodiments, the enzymatic activity may be endonuclease activity, integrase activity, nickase activity, exonuclease activity, transposase activity and / or excision activity. In some cases, the effector may be catalytically inactive. [0038] Assays which leverage the transcollateral cleavage properties of programmable nuclease enzymes (e.g., CRISPR-Cas enzymes) are often referred to herein as DNA endonuclease targeted CRISPR trans reporter (DETECTR) reactions. As used herein, detection of reporter cleavage (directly or indirectly) to determine the presence of a target nucleic acid sequence may be referred to as “DETECTR”. [0039] As used herein, the term “mutation” refers to a variation (e.g., a nucleotide substitution, an indel or a rearrangement) that is present or deemed as being likely to be present in a nucleic acid sample. It can be used interchangeably with a “genetic variation.” A mutation can be any alteration in a nucleotide sequence in the genome of an organism. A mutation can also include a germline mutation, wherein the mutation can be inherited by subsequent generations of the organism. In some other instances, the mutation can be a de novo or somatic mutation; a mutation not inherited from either parent. The mutation can include a nucleotide variant or a point mutation. Mutations may also include, but are not limited to, base substitutions (SNPs), insertions, deletions, gene fusions (at junctions), transversions, or duplications. [0040] As used herein, the term “point mutation,” refers to a mutation of a single nucleotide or nucleotide within a DNA sequence of the genome of an organism. Point mutations can have effects on the downstream protein product that can different consequences on the protein product depending on the specifics of the mutation. Mutations can include, but are not limited to, nonsense mutations, missense mutations, silent mutations, insertions, or deletions. [0041] As used herein, the term “nucleotide variant,” refers to any mutation that can comprise a sequence variant of a gene. It can comprise a sequence wherein the sequence can differ from the reference gene sequence by any number of nucleotides. A nucleotide variant can comprise at least 1 point mutation. [0042] As used herein, the term “missense mutation,” refers to a point mutation in which a single nucleotide or nucleotide substitution results in the change of an amino acid identity in the protein product of a given gene. The mutation can occur in the coding sequence of a given gene and can occur at any one of the three positions of a codon in a given coding sequence. [0043] As used herein, the term “non-sense mutation,” refers to any change in the genomic sequence that introduces a premature stop codon, causing the resulting protein product to be abnormally shortened. In some cases, a non-sense mutation causes a loss of function in the protein product. [0044] As used herein, the term “nonstop mutation, refers to a point mutation that occurs within a stop codon. Nonstop mutations cause the continued translation of an mRNA strand into an untranslated region, resulting in a polypeptide of an inappropriate length for a given gene. A non-stop mutation can render the protein product of a gene as non-functional. [0045] As used herein, the term “synonymous mutation,” refers to a substitution or point mutation of a nucleotide in an exon of a gene that codes for a protein, such that the produced amino acid sequence is not altered. Synonymous substitutions and mutations affecting noncoding DNA can be considered silent mutations; however, it is not always the case that the mutation is silent. A synonymous mutation can affect transcription, splicing, mRNA transport, and translation, any of which could alter the resulting phenotype, rendering the synonymous mutation non-silent. [0046] As used herein, the term “non-synonymous mutation,” refers to a nucleotide mutation that alters the amino acid sequence of a protein product of a given gene. As non- synonymous mutation can result in a functional change in the protein product of a given gene. Introduction [0047] The present disclosure is generally related to genotyping using site-directed effector proteins (e.g., programmable nucleases) and more particularly relates to systems, methods, and compositions for detecting nucleotide variations using site-directed effector proteins. Also provided are methods and compositions for SNP genotyping an organism using site-directed effector proteins. While the present disclosure provides exemplary systems, methods, and compositions for SNP genotyping, one of ordinary skill in the art will appreciate that this is not intended to be limiting and the systems, compositions, and methods disclosed herein may be used to detect other genetic variations including, but not limited to, base substitutions (e.g., SNPs), insertions, deletions, gene fusions (e.g., at junctions), or the like. [0048] For example, provided herein, in certain embodiments, are methods of assaying for a target nucleic acid molecule comprising a nucleotide variant at a position of interest, the method comprising (a) contacting a sample to: a composition comprising an effector protein and a guide nucleic acid; and a reporter, and detecting the presence or absence of the target nucleic acid comprising the nucleotide variant by assaying for a signal produced by the effector protein; and (c) comparing the signal to a control signal produced by contacting the composition and reporter to a control nucleic acid molecule not comprising the nucleotide variant, but that is otherwise identical to the target nucleic acid molecule, at least apart from a variation of less than four nucleotides. [0049] Also provided herein, in certain embodiments, are methods for determining a single nucleotide polymorphism (SNP) genotype in an organism, comprising: assaying for at least one target nucleic acid comprising the SNP in a sample by assaying for a first signal produced by a first effector protein; assaying for at least one target nucleic acid not comprising the SNP in the sample by assaying for a second signal produced by a second effector protein; and comparing the first signal and the second signal. [0050] Also disclosed herein are non-naturally occurring compositions and systems which may be used for determining a nucleotide variant at a position of interest in a target nucleic acid, or for SNP genotyping an organism. In some cases, the compositions and systems comprising at least one of an engineered Cas protein and an engineered guide nucleic acid, which may simply be referred to herein as a Cas protein and a guide nucleic acid, respectively. In general, an engineered Cas protein and an engineered guide nucleic acid refer to a Cas protein and a guide nucleic acid, respectively, that are not found in nature. In some instances, systems and compositions comprise at least one non-naturally occurring component. For example, compositions and systems may comprise a guide nucleic acid, wherein the sequence of the guide nucleic acid is different or modified from that of a naturally-occurring guide nucleic acid. In some instances, compositions and systems comprise at least two components that do not naturally occur together. For example, compositions and systems may comprise a guide nucleic acid comprising a repeat region and a spacer region which do not naturally occur together. Also, by way of example, composition and systems may comprise a guide nucleic acid and a Cas protein that do not naturally occur together. Conversely, and for clarity, a Cas protein or guide nucleic acid that is “natural,” “naturally-occurring,” or “found in nature” includes Cas proteins and guide nucleic acids from cells or organisms that have not been genetically modified by a human or machine. [0051] In some instances, the guide nucleic acid comprises a non-natural nucleotide sequence. In some instances, the non-natural sequence is a nucleotide sequence that is not found in nature. The non-natural sequence may comprise a portion of a naturally-occurring sequence, wherein the portion of the naturally-occurring sequence is not present in nature absent the remainder of the naturally-occurring sequence. In some instances, the guide nucleic acid comprises two naturally-occurring sequences arranged in an order or proximity that is not observed in nature. In some instances, compositions and systems comprise a ribonucleotide complex comprising a CRISPR/Cas effector protein and a guide nucleic acid that do not occur together in nature. Engineered guide nucleic acids may comprise a first sequence and a second sequence that do not occur naturally together. For example, an engineered guide nucleic acid may comprise a sequence of a naturally-occurring repeat region and a spacer region that is complementary to a naturally-occurring eukaryotic sequence. The engineered guide nucleic acid may comprise a sequence of a repeat region that occurs naturally in an organism and a spacer region that does not occur naturally in that organism. An engineered guide nucleic acid may comprise a first sequence that occurs in a first organism and a second sequence that occurs in a second organism, wherein the first organism and the second organism are different. The guide nucleic acid may comprise a third sequence disposed at a 3’ or 5’ end of the guide nucleic acid, or between the first and second sequences of the guide nucleic acid. For example, an engineered guide nucleic acid may comprise a naturally occurring gRNA and tracrRNA coupled by a linker sequence. [0052] In some instances, compositions and systems described herein comprise an engineered Cas protein that is similar to a naturally occurring Cas protein. The engineered Cas protein may lack a portion of the naturally occurring Cas protein. The Cas protein may comprise a mutation relative to the naturally-occurring Cas protein, wherein the mutation is not found in nature. The Cas protein may also comprise at least one additional amino acid relative to the naturally-occurring Cas protein. For example, the Cas protein may comprise an addition of a nuclear localization signal relative to the natural occurring Cas protein. In certain embodiments, the nucleotide sequence encoding the Cas protein is codon optimized (e.g., for expression in a eukaryotic cell) relative to the naturally occurring sequence. [0053] In some instances, compositions and systems provided herein comprise a multi- vector system encoding a Cas protein and a guide nucleic acid described herein, wherein the guide nucleic acid and the Cas protein are encoded by the same or different vectors. In some embodiments, the engineered guide and the engineered Cas protein are encoded by different vectors of the system. I. Methods of Detecting a Nucleotide Variant [0054] Disclosed herein, in some instances, are methods of assaying for a target nucleic acid molecule comprising a nucleotide variant at a position of interest, comprising (a) contacting a sample to: a composition comprising an effector protein and a guide nucleic acid; and a reporter, and detecting the presence or absence of the target nucleic acid comprising the nucleotide variant by assaying for a signal produced by the effector protein; and (c) comparing the signal to a control signal produced by contacting the composition and reporter to a control nucleic acid molecule not comprising the nucleotide variant, but that is otherwise identical to the target nucleic acid molecule, at least apart from a variation of less than four nucleotides. [0055] In some cases, detecting the presence or absence of the target nucleic acid is carried out in a detection reaction. In some cases, the detection reaction comprises assaying for a signal produced by an effector protein. In some cases, the assaying for a signal produced by an effector protein comprises assaying for a signal, or change in signal, produced by trans cleavage of the reporter by the effector protein, wherein the trans cleavage is activated upon hybridization of the guide nucleic acid to the target nucleic acid molecule comprising the nucleotide variant. In some cases, assaying for a signal produced by an effector protein comprises contacting the sample to a complex comprising the effector protein and a guide nucleic acid comprising a segment that is reverse complementary to a segment of the target nucleic acid. In some cases, the complex exhibits sequence independent cleavage (e.g., trans cleavage) and/or sequence dependent cleavage (e.g., cis cleavage) upon binding to the target nucleic acid. In some cases, the complex trans cleaves at least one reporter nucleic acid (also referred to herein as “detectable moiety”, “nucleic acid of the reporter”, or “reporter”) of a population of reporter nucleic acids, wherein the cleavage indicates a presence of the target nucleic acid in the sample and wherein absence of the cleavage indicates an absence of the target nucleic acid in the sample. In some embodiments, the effector protein cleavage activity is enhanced when paired to a specific guide sequence. In some embodiments, a specific guide sequence and effector protein combination may be selected to enhance selectivity of target guide nucleic acid. In some embodiments, detecting the presence or absence of the target nucleic acid comprises the specific combination of guide nucleic acids and effector proteins as disclosed herein. In some embodiments, detecting the presence or absence of the target nucleic acid comprises the specific combination of guide nucleic acids and effector proteins as disclosed in Table 4. [0056] In some embodiments, the detection reaction detects the presence or absence of a target nucleic acid comprising nucleotide variant within a window of time. In some embodiments, the detection reaction time is about 3 minutes to about 30 minutes. In some embodiments, the detection reaction time is about 3 minutes to about 5 minutes, about 3 minutes to about 7 minutes, about 3 minutes to about 10 minutes, about 3 minutes to about 13 minutes, about 3 minutes to about 15 minutes, about 3 minutes to about 17 minutes, about 3 minutes to about 20 minutes, about 3 minutes to about 25 minutes, about 3 minutes to about 30 minutes, about 5 minutes to about 7 minutes, about 5 minutes to about 10 minutes, about 5 minutes to about 13 minutes, about 5 minutes to about 15 minutes, about 5 minutes to about 17 minutes, about 5 minutes to about 20 minutes, about 5 minutes to about 25 minutes, about 5 minutes to about 30 minutes, about 7 minutes to about 10 minutes, about 7 minutes to about 13 minutes, about 7 minutes to about 15 minutes, about 7 minutes to about 17 minutes, about 7 minutes to about 20 minutes, about 7 minutes to about 25 minutes, about 7 minutes to about 30 minutes, about 10 minutes to about 13 minutes, about 10 minutes to about 15 minutes, about 10 minutes to about 17 minutes, about 10 minutes to about 20 minutes, about 10 minutes to about 25 minutes, about 10 minutes to about 30 minutes, about 13 minutes to about 15 minutes, about 13 minutes to about 17 minutes, about 13 minutes to about 20 minutes, about 13 minutes to about 25 minutes, about 13 minutes to about 30 minutes, about 15 minutes to about 17 minutes, about 15 minutes to about 20 minutes, about 15 minutes to about 25 minutes, about 15 minutes to about 30 minutes, about 17 minutes to about 20 minutes, about 17 minutes to about 25 minutes, about 17 minutes to about 30 minutes, about 20 minutes to about 25 minutes, about 20 minutes to about 30 minutes, or about 25 minutes to about 30 minutes. In some embodiments, the detection reaction time is about 3 minutes, about 5 minutes, about 7 minutes, about 10 minutes, about 13 minutes, about 15 minutes, about 17 minutes, about 20 minutes, about 25 minutes, or about 30 minutes. In some embodiments, the detection reaction time is at least about 3 minutes, about 5 minutes, about 7 minutes, about 10 minutes, about 13 minutes, about 15 minutes, about 17 minutes, about 20 minutes, or about 25 minutes. In some embodiments, the detection reaction time is at most about 5 minutes, about 7 minutes, about 10 minutes, about 13 minutes, about 15 minutes, about 17 minutes, about 20 minutes, about 25 minutes, or about 30 minutes. In some embodiments, the detection reaction time less than about 5 minutes to about 30 minutes. In some embodiments, the detection reaction time less than about 5 minutes to about 7 minutes, about 5 minutes to about 10 minutes, about 5 minutes to about 13 minutes, about 5 minutes to about 15 minutes, about 5 minutes to about 17 minutes, about 5 minutes to about 20 minutes, about 5 minutes to about 25 minutes, about 5 minutes to about 30 minutes, about 7 minutes to about 10 minutes, about 7 minutes to about 13 minutes, about 7 minutes to about 15 minutes, about 7 minutes to about 17 minutes, about 7 minutes to about 20 minutes, about 7 minutes to about 25 minutes, about 7 minutes to about 30 minutes, about 10 minutes to about 13 minutes, about 10 minutes to about 15 minutes, about 10 minutes to about 17 minutes, about 10 minutes to about 20 minutes, about 10 minutes to about 25 minutes, about 10 minutes to about 30 minutes, about 13 minutes to about 15 minutes, about 13 minutes to about 17 minutes, about 13 minutes to about 20 minutes, about 13 minutes to about 25 minutes, about 13 minutes to about 30 minutes, about 15 minutes to about 17 minutes, about 15 minutes to about 20 minutes, about 15 minutes to about 25 minutes, about 15 minutes to about 30 minutes, about 17 minutes to about 20 minutes, about 17 minutes to about 25 minutes, about 17 minutes to about 30 minutes, about 20 minutes to about 25 minutes, about 20 minutes to about 30 minutes, or about 25 minutes to about 30 minutes. In some embodiments, the detection reaction time less than about 5 minutes, about 7 minutes, about 10 minutes, about 13 minutes, about 15 minutes, about 17 minutes, about 20 minutes, about 25 minutes, or about 30 minutes. In some embodiments, the detection reaction time less than at least about 5 minutes, about 7 minutes, about 10 minutes, about 13 minutes, about 15 minutes, about 17 minutes, about 20 minutes, or about 25 minutes. In some embodiments, the detection reaction time less than at most about 7 minutes, about 10 minutes, about 13 minutes, about 15 minutes, about 17 minutes, about 20 minutes, about 25 minutes, or about 30 minutes. [0057] In some embodiments, the detection reaction detects the presence or absence of a target nucleic acid comprising nucleotide variant within a purified sample, or fragment thereof. In some embodiments, the detection reaction detects the presence or absence of a target nucleic acid comprising nucleotide variant within a non-purified sample, or fragment thereof. [0058] In some embodiments, the detection assay comprises direct detection. In some embodiments, direct detection comprises detection of the target nucleic acid within a crude or unprocessed clinical sample. In some embodiments, a crude or unprocessed sample is a non- purified sample. In some embodiments a crude or unprocessed sample comprises a sample directly collected from an organism. In some embodiments, the crude or unprocessed sample is collected from a buccal swab. In some embodiments, the crude or unprocessed sample is saliva directly collected from the organism. In some embodiments, the saliva directly collected from the organism comprises the DNA or RNA target nucleic acid for detection assay. [0059] In some embodiments, the detection assay comprises sample processing prior to detection. In some embodiments, sample processing prior to detection comprises purifying the sample collected from the organism. In some embodiments, the crude, unprocessed, or non- purified sample can be purified or processed. In some embodiments, the non-purified sample is purified prior to pre-amplification or pre-amplification method. In some embodiments, the detection assay comprises pre-amplification as disclosed herein. [0060] In some cases, the sample comprises the target nucleic acid and at least one non- target nucleic acid comprising less than 100% sequence identity to the target nucleic acid, but no less than 80% sequence identity to the target nucleic acid. In some cases, the sample comprises the target nucleic acid and at least one non-target nucleic acid comprising less than 100% sequence identity to the target nucleic acid, but no less than 90% sequence identity to the target nucleic acid. In some cases, the sample comprises the target nucleic acid and at least one non- target nucleic acid comprising less than 100% sequence identity to the target nucleic acid, but no less than 95% sequence identity to the target nucleic acid. In some cases, the sample comprises the target nucleic acid and at least one non-target nucleic acid comprising less than 100% sequence identity to the target nucleic acid, but varying from the target nucleic acid at less than four, three, or two nucleotides. In some cases, the sample comprises a plurality of the non-target nucleic acids, or amplicons thereof, and a plurality of target nucleic acids, or amplicons thereof. In some cases, a complex formed by the effector protein and the guide nucleic acid does not bind to or cleave a substantial portion of the non-target nucleic acids. In some cases, the complex binds to and cleaves less than 50%, 40%, 30%, 20%, 10% or 5% of the plurality of non-target nucleic acids. In some cases, the complex binds to and cleaves greater than 50%, 60%, 70%, 80%, 90%, or 100% of the plurality of target nucleic acids. [0061] In some cases, signal produced for the target nucleic acid is compared to a signal produced for a control nucleic acid, such as in a control reaction. In some embodiments, detection comprises assaying for the presence of the target nucleic acid not comprising the nucleotide variant, wherein the presence of the target nucleic acid not comprising the nucleotide variant elicits the control signal as disclosed herein. In some cases, the control nucleic acid molecule is otherwise identical to the target nucleic acid molecule, apart from a variation of less 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 nucleotides. In some cases, the control nucleic acid molecule is otherwise identical to the target nucleic acid molecule, apart from a variation of less than four nucleotides. In some cases, the control nucleic acid molecule is otherwise identical to the target nucleic acid molecule, apart from a variation of less than three nucleotides. In some cases, the control nucleic acid molecule is otherwise identical to the target nucleic acid molecule, apart from a variation of less than one nucleotide. In some cases, the control signal is produced by a control reaction, which comprises contacting a composition comprising a control effector protein and a control guide nucleic acid to a control nucleic acid molecule. In some cases, the control effector protein is 100% identical to the effector protein. In some cases, the control guide nucleic acid is 100% identical to the guide nucleic acid. In some cases, the control reaction is performed in the same, or substantially the same, reaction conditions as the detection reaction. [0062] In some cases, the nucleotide variant at the position of interest is a point mutation. In some embodiments, the point mutation in the target nucleic acid molecule is relative to an otherwise identical target nucleic acid molecule. In some cases, the nucleotide variant is a polymorphism (e.g., an SNP) or somatic mutation. In some embodiments, the point mutation in the target nucleic acid molecule is a SNP. In some embodiments, the SNP is silent, disease- related, or disease-causing. In some cases, the nucleotide variant (e.g., the SNP) is associated with a phenotype of the sample or a phenotype of the organism from which the sample was taken. The nucleotide variant (e.g., the SNP) in some cases, is associated with altered phenotype from a wild type phenotype. Often, the nucleotide variant (e.g., the SNP) is associated with a disease such as cancer or a genetic disorder. In some cases, the nucleotide variant is encoded in the sequence of the target nucleic acid from the germline of an organism or is encoded in a target nucleic acid from a diseased cell, such as a cancer cell. In some cases, the nucleotide variant comprises a synonymous substitution or a nonsynonymous substitution. In some cases, the nonsynonymous substitution is a missense substitution or a nonsense point mutation. In some cases, the nucleotide variant comprises a deletion, for example a deletion of one or more base pairs from an exon sequence. The deletion can be associated with a phenotype of the sample or a phenotype of the organism from which the sample was taken. The deletion, in some cases, is associated with altered phenotype from wild type phenotype. In some cases, the deletion is associated with a disease such as cancer or a genetic disorder. The deletion can be encoded in the sequence of a target nucleic acid from the germline of an organism or can be encoded in a target nucleic acid from a diseased cell, such as a cancer cell. In some cases, the target nucleic acid is a DNA or RNA. The methods disclosed herein can be used to diagnose or identify diseases associated with target nucleic acid. [0063] In some cases, the target nucleic acid molecule is, or is encoded by, a PNPLA3 gene (NCBI Reference Sequence: NG_008631.1), a cDNA thereof, or a fragment thereof. In some cases, the PNPLA3 gene comprises a substitution of a C with a G at nucleotide position 444 of a wild-type PNPLA3 gene cDNA of SEQ ID NO: 384. In some embodiments, the PNPLA3 gene encodes a PNPLA3 protein comprising an I to M substitution at amino acid position of 148 of a wild-type PNPLA3 protein of SEQ ID NO: 385.

[0064] In some cases, the target nucleic acid comprised in a sample is purified or non- purified prior to detection assay to detect the presence or absence of the target nucleic acid comprising the nucleotide variant. In some cases, the target nucleic acid comprised in a sample is amplified or prior to detection assay to detect the presence or absence of the target nucleic acid comprising the nucleotide variant. In some embodiments, the assays disclosed herein are performed with a fragment of a sample. In some embodiments, the assays disclosed herein are performed multiple times with multiple fragments of a single sample. In some embodiments, the assays performed with multiple fragments of a single sample are referred to as “repeats”. In some embodiments, repeats are performed in single or separate reactions. [0065] In some embodiments, the method of assaying for the nucleotide variation further comprises determining whether an organism from which the sample is derived is homozygous or heterozygous for the nucleotide variation. In some embodiments, determining whether the organism is homozygous or heterozygous for the nucleotide variation comprises assaying for a plurality of the target nucleic acids in the sample in a first reaction, assaying for a plurality of non-target nucleic acids (e.g., not comprising the nucleotide variation) in the sample in a second reaction, and comparing signals produced by the first and second reactions. In some embodiments, determining whether the organism is homozygous or heterozygous for the nucleotide variation comprises identifying the organism as heterozygous for the mutation if the level of the signal produced by the first reaction is higher or lower than the level of the signal produced by the second reaction. In some embodiments, determining whether the organism is homozygous or heterozygous for the mutation comprises identifying the organism as homozygous for the variation if the levels of signals produced by the first and second reactions are about equal. II. Methods of Genotyping Using Cas Effector Protein Assays [0066] Provided herein, in some instances, are methods for determining a genomic variant in an organism. In an exemplary embodiment, provided herein are methods for determining a single nucleotide polymorphism (SNP) or other genomic variant genotype in an organism, comprising: (a) assaying for at least one target nucleic acid comprising the SNP or other genomic variant in a sample by assaying for a first signal produced by a first effector protein; (b) assaying for at least one target nucleic acid not comprising the SNP or other genomic variant in the sample by assaying for a second signal produced by a second effector protein; and (c) comparing the first signal and the second signal. In some cases, the first or second effector protein comprise any effector protein disclosed herein. In some cases, the first or second guide nucleic acid comprise any guide nucleic acid disclosed herein. [0067] In some embodiments, assaying for the target nucleic acid comprising the genomic variant (e.g., SNP, somatic mutation, insertion, deletion, or other genomic variant described herein or understood by one of ordinary skill in the art based on the teachings herein), or the target nucleic acid not comprising the genomic variant (e.g., SNP), comprises performing a cleavage assay disclosed herein (e.g., a trans cleavage assay disclosed herein). In some instances, assaying for at least one target nucleic acid comprising the genomic variant (e.g., SNP) comprises: (i) contacting at least a first portion of the sample to a first composition comprising a first effector protein, a first guide nucleic acid, and a first reporter; and (ii) detecting the presence or absence of a target nucleic acid comprising the genomic variant (e.g., SNP) by assaying for a first signal, or change in first signal, produced by trans cleavage of the first reporter by the first effector protein, wherein the trans cleavage is activated upon hybridization of the first guide nucleic acid to the target nucleic acid molecule comprising the genomic variant (e.g., SNP). In some instances, assaying for at least one target nucleic acid not comprising the genomic variant (e.g., SNP) comprises: (i) contacting at least a second portion of the sample to: a second composition comprising a second effector protein, a second guide nucleic acid, and a second reporter; and (ii) detecting the presence or absence of a target nucleic acid not comprising the genomic variant (e.g., SNP) by assaying for a second signal, or change second in signal, produced by trans cleavage of the second reporter by the second effector protein, wherein the trans cleavage is activated upon hybridization of the second guide nucleic acid to the target nucleic acid molecule not comprising the genomic variant (e.g., SNP). [0068] In some cases, the cleavage assays are performed multiple times with multiple fragments of a single sample. In some embodiments, the assays performed with multiple fragments of a single sample are referred to as “repeats.” In some embodiments, repeats are performed in single or separate reactions. In some cases, the assaying for the at least one target nucleic acid comprising the genomic variant (e.g., SNP) is performed with a first fragment of the sample. In some cases, the assaying for the at least one target nucleic acid not comprising the genomic variant (e.g., SNP) is performed with a second fragment of the sample. In some cases, the assaying for the at least one target nucleic acid comprising the genomic variant (e.g., SNP) and the assaying for the at least one target nucleic acid not comprising the snip are performed on a single fragment of the sample. In some cases, the assaying for the at least one target nucleic acid comprising the genomic variant (e.g., SNP) and the assaying for the at least one target nucleic acid not comprising the genomic variant (e.g., SNP) are performed in a single reaction volume. [0069] In some cases, the assaying for the at least one target nucleic acid comprising the SNP comprises assaying for a plurality of nucleic acids comprising the genomic variant (e.g., SNP). In some instances, the assaying for the at least one target nucleic acid not comprising the SNP comprises assaying for a plurality of target nucleic acids not comprising the genomic variant (e.g., SNP). In some cases, comparing the first signal and the second signal comprises comparing the signal produced for the plurality of nucleic acids comprising the genomic variant (e.g., SNP) to the signal produced for the plurality of nucleic acids not comprising the genomic variant (e.g., SNP). In some cases, the signal is a fluorescent signal. In some cases, comparing the first signal to the second signal comprises determining the level of fluorescence produced for the plurality of nucleic acids comprising the genomic variant (e.g., SNP) and comparing it to the level of fluorescence produced for the plurality of the nucleic acids not comprising the genomic variant (e.g., SNP). [0070] In some cases, the method comprises determining whether the organism is homozygous or heterozygous for the genomic variant (e.g., SNP) or for the target nucleic acid not comprising the genomic variant (e.g., SNP). In some cases, the target nucleic acid comprising the genomic variant (e.g., SNP) is a mutant form of a gene (e.g., a mutant allele), or a fragment thereof, and the target nucleic acid not comprising the genomic variant (e.g., SNP) is a wild type form of the same gene (e.g., a wild type allele), or a fragment thereof. In some embodiments, determining whether the organism is homozygous or heterozygous for the genomic variant (e.g., SNP) comprises comparing a level of the first detectable signal to a level of the second detectable signal. In some embodiments, determining whether the organism is homozygous or heterozygous for the genomic variant (e.g., SNP) comprises identifying the organism as heterozygous for the genomic variant (e.g., SNP) if the level of the first detectable signal is about equal to the level of the second detectable signal. In some embodiments, determining whether the organism is homozygous or heterozygous for the genomic variant (e.g., SNP) comprises identifying the organism as homozygous for the genomic variant (e.g., for the mutant allele) if the level of the first detectable signal is higher than the level of the second detectable signal. In some embodiments, determining whether the organism is homozygous or heterozygous for the genomic variant (e.g., SNP) comprises identifying the organism as homozygous for the target nucleic acid not comprising the genomic variant (e.g., the wild type allele) if the level of the second detectable signal is higher than the level of the first detectable signal. [0071] In some cases, the signal is a fluorescent signal. In some cases, the assaying for the at least one target nucleic acid comprising the genomic variant (e.g., SNP) comprises assaying for fluorescent signal produced for a plurality of nucleic acids comprising the genomic variant (e.g., SNP). In some instances, the assaying for the at least one target nucleic acid not comprising the genomic variant (e.g., SNP) comprises assaying for a fluorescent signal produced for a plurality of target nucleic acids not comprising the genomic variant (e.g., SNP). In some cases, comparing the first signal to the second signal comprises determining the level of fluorescence produced for the plurality of nucleic acids comprising the genomic variant (e.g., SNP) and comparing it to the level of fluorescence produced for the plurality of the nucleic acids not comprising the genomic variant (e.g., SNP). In some cases, the comparing the levels of fluorescence comprises determining a ratio of normalized fluorescence produced for the target nucleic acids comprising the genomic variant (e.g., SNP) and the target nucleic acids not comprising the genomic variant (e.g., SNP). In some cases, the ratio of normalized fluorescence is according to the following formula:

[0072] where X1 is a normalized value corresponding to the fluorescence produced for the plurality of nucleic acids not comprising the genomic variant (e.g., SNP), and X₂ is a normalized value corresponding to the fluorescence produced for the plurality of nucleic acids comprising the genomic variant (e.g., SNP). [0073] In some embodiments, the target nucleic acid comprised in a sample is purified or non-purified prior to detection assay for genomic variant (e.g., SNP) genotyping. In some embodiments, the target nucleic acid comprised in a sample is amplified or prior to detection assay for genomic variant (e.g., SNP) genotyping. In some embodiments, the assays disclosed herein are performed with a fragment of a sample. a. Amplification Techniques [0074] In some instances, methods of assaying for a target nucleic acid molecule comprising a nucleotide variant at a position of interest, comprise amplifying a target nucleic acid molecule, and/or amplifying a nucleic acid molecule in a sample to produce a target nucleic acid molecule. In some embodiments, methods of amplifying disclosed herein can be considered pre-amplification methods, as they occur prior to or concurrently with detecting the presence or absence of the target nucleic acid molecule. In some embodiments, methods of amplifying a target nucleic acid molecule prior to nucleotide variant detection comprise amplifying the target nucleic acid comprising the SNP, the target nucleic acid not comprising the SNP, or a combination thereof. In some embodiments, methods of amplifying a target nucleic acid molecule prior to nucleotide variant detection comprise amplifying a purified genomic sample, or a fraction thereof. In some embodiments, methods of amplifying a target nucleic acid molecule prior to nucleotide variant detection comprise amplifying a non-purified genomic sample, or a fraction thereof. In some embodiments, method of amplifying a purified genomic sample, or a fraction thereof, are the same as methods of amplifying a non-purified genomic sample, or a fraction thereof. In some embodiments, method of amplifying a purified genomic sample, or a fraction thereof, are different than methods of amplifying a non-purified genomic sample, or a fraction thereof. In some embodiments, amplifying a purified genomic sample, or a fraction thereof, prior to nucleotide variant detection improves detection of target nucleic acid molecule comprising a nucleotide variant at a position of interest. In some embodiments, amplifying a non-purified genomic sample, or a fraction thereof, prior to nucleotide variant detection improves detection of target nucleic acid molecule comprising a nucleotide variant at a position of interest. [0075] In some embodiments, methods of amplifying a target nucleic acid molecule prior to nucleotide variant detection comprise amplifying the target nucleic acid using any of the compositions or systems described herein. In some embodiments, amplifying may comprise changing the temperature of the amplification reaction, also known as thermal amplification (e.g., PCR). In some embodiments, amplifying may be performed at essentially one temperature, also known as isothermal amplification. In some embodiments, amplifying may improve at least one of sensitivity, specificity, or accuracy of the detection of the target nucleic acid. In some embodiments, some cases, some DNA samples may be pre-amplified prior to detection. In some embodiments, In some cases, some RNA samples may be pre-amplified prior to detection. [0076] In some embodiments, amplifying may comprise subjecting a target nucleic acid to an amplification reaction selected from transcription mediated amplification (TMA), helicase dependent amplification (HDA), or circular helicase dependent amplification (cHDA), strand displacement amplification (SDA), recombinase polymerase amplification (RPA), loop mediated amplification (LAMP), exponential amplification reaction (EXPAR), rolling circle amplification (RCA), ligase chain reaction (LCR), simple method amplifying RNA targets (SMART), single primer isothermal amplification (SPIA), multiple displacement amplification (MDA), nucleic acid sequence based amplification (NASBA), hinge-initiated primer-dependent amplification of nucleic acids (HIP), nicking enzyme amplification reaction (NEAR), and improved multiple displacement amplification (IMDA). [0077] In some embodiments, amplification of the target nucleic acid comprises modifying the sequence of the target nucleic acid. For example, amplification may be used to insert a PAM sequence into a target nucleic acid that lacks a PAM sequence. In some cases, amplification may be used to increase the homogeneity of a target nucleic acid in a sample. For example, amplification may be used to remove a nucleic acid variation that is not of interest in the target nucleic acid sequence. [0078] In some embodiments, amplification or pre-amplification conditions for rapid detection of a target nucleic acid are adjusted for purified and non-purified samples. In some embodiments, amplification or pre-amplification conditions for rapid detection of a target nucleic acid are adjusted for different target nucleic acid. In some embodiments, amplification or pre- amplification conditions for rapid detection of presence or absence of a target nucleic acid are adjusted. In some embodiments, adjustment of amplification or pre-amplification conditions for rapid detection of presence or absence of a target nucleic acid changes time to result (minutes). The time to result of a detection (DETECTR) assay using different pre-amplification conditions in purified and non-purified samples varied. Time to result is measured as the time at which exponential amplification occurs. In some embodiments, variation of pre-amplification conditions enable pre-amplification times of less than 20 minutes. In some embodiments, variation of pre-amplification conditions enable pre-amplification times of less than 15 minutes. In some embodiments, rapid detection of absence of a target nucleic acid is a negative control (NTC). In some embodiments, amplification conditions enable amplification of a target nucleic acid in less than 20 minutes. In some embodiments, amplification conditions enable amplification of a target nucleic acid in less than 15 minutes. In some embodiments, amplification conditions enable amplification of a target nucleic acid in less than 20 minutes, and detection of the target nucleic acid in about 15 minutes. In some embodiments, amplification conditions enable amplification of a target nucleic acid in in less than 15 minutes, and detection of the target nucleic acid in about 15 minutes. FIG.1 illustrates an assay workflow for detecting at-risk alleles of a target gene in about 30 minutes using a Cas12 effector protein. A sample, for example purified genomic DNA (“gDNA”), undergoes pre-amplification for about 15 minutes followed by detection with an effector protein, for example a Cas12 effector protein, for about 15 minutes. FIG.2 illustrates an assay workflow for detecting at-risk alleles of a target gene in about 36 minutes using a Cas12 effector protein. A sample, for example the non-purified or crude sample as disclosed herein, undergoes pre-amplification for about 20 minutes followed by detection with an effector protein, for example a Cas12 effector protein, for about 15 minutes. [0079] In some embodiments, sample pre-amplification enables detection of the target nucleic acid in less than 30 minutes. In some embodiments, following amplification, samples containing about 240 copies of target nucleic acid per reaction are detected in less than 30 minutes. In some embodiments, following amplification, samples containing about 240 copies of target nucleic acid (DNA or RNA) per reaction are detected in less than 30 minutes. In some embodiments, following amplification, samples containing about 240 copies of genomic DNA per reaction are detected in less than 30 minutes. In some embodiments, following amplification, samples containing about 240 copies of genomic DNA per reaction are detected for wild type allele, at-risk allele, or non-risk allele of PNPLA3 in less than 30 minutes. In some embodiments, following amplification, samples containing about 240 copies of genomic DNA per reaction are detected for wild type allele, at-risk allele, or non-risk allele based on fluorescence signal. In some embodiments, fluorescence signal data collected from pre-amplified samples was used to genotype the samples as homozygous or heterozygous for the PNPLA3 SNPs. In some embodiments, fluorescence signal data collected from pre-amplified samples containing synthetic control nucleic acids were assayed to determine a baseline fluorescence for each PNPLA3 genotype. FIG.3 shows the results of a LAMP and DETECTR assay measuring synthetic control samples for different genetic combinations of PNPLA3 alleles. In some embodiments, fluorescence signal data collected from pre-amplified samples was analyzed to determine threshold fluorescence ratios differentiate wild type, mutant, and heterozygous phenotypes. In some embodiments, fluorescence signal data collected from pre-amplified samples was analyzed to detect the presence or absence of an at-risk PNPLA3 allele. In some embodiments, fluorescence signal data collected from pre-amplified samples was used to calculate fluorescence intensity ratios to distinguish between wild type, heterozygous, and at-risk sequences. [0080] In some embodiments, the amplification reaction time may take about 1 minute to about 40 minutes. In some embodiments, the amplification reaction time is about 1 minute to about 40 minutes. In some embodiments, the amplification reaction time is about 1 minute to about 3 minutes, about 1 minute to about 5 minutes, about 1 minute to about 7 minutes, about 1 minute to about 10 minutes, about 1 minute to about 13 minutes, about 1 minute to about 15 minutes, about 1 minute to about 17 minutes, about 1 minute to about 20 minutes, about 1 minute to about 25 minutes, about 1 minute to about 30 minutes, about 1 minute to about 40 minutes, about 3 minutes to about 5 minutes, about 3 minutes to about 7 minutes, about 3 minutes to about 10 minutes, about 3 minutes to about 13 minutes, about 3 minutes to about 15 minutes, about 3 minutes to about 17 minutes, about 3 minutes to about 20 minutes, about 3 minutes to about 25 minutes, about 3 minutes to about 30 minutes, about 3 minutes to about 40 minutes, about 5 minutes to about 7 minutes, about 5 minutes to about 10 minutes, about 5 minutes to about 13 minutes, about 5 minutes to about 15 minutes, about 5 minutes to about 17 minutes, about 5 minutes to about 20 minutes, about 5 minutes to about 25 minutes, about 5 minutes to about 30 minutes, about 5 minutes to about 40 minutes, about 7 minutes to about 10 minutes, about 7 minutes to about 13 minutes, about 7 minutes to about 15 minutes, about 7 minutes to about 17 minutes, about 7 minutes to about 20 minutes, about 7 minutes to about 25 minutes, about 7 minutes to about 30 minutes, about 7 minutes to about 40 minutes, about 10 minutes to about 13 minutes, about 10 minutes to about 15 minutes, about 10 minutes to about 17 minutes, about 10 minutes to about 20 minutes, about 10 minutes to about 25 minutes, about 10 minutes to about 30 minutes, about 10 minutes to about 40 minutes, about 13 minutes to about 15 minutes, about 13 minutes to about 17 minutes, about 13 minutes to about 20 minutes, about 13 minutes to about 25 minutes, about 13 minutes to about 30 minutes, about 13 minutes to about 40 minutes, about 15 minutes to about 17 minutes, about 15 minutes to about 20 minutes, about 15 minutes to about 25 minutes, about 15 minutes to about 30 minutes, about 15 minutes to about 40 minutes, about 17 minutes to about 20 minutes, about 17 minutes to about 25 minutes, about 17 minutes to about 30 minutes, about 17 minutes to about 40 minutes, about 20 minutes to about 25 minutes, about 20 minutes to about 30 minutes, about 20 minutes to about 40 minutes, about 25 minutes to about 30 minutes, about 25 minutes to about 40 minutes, or about 30 minutes to about 40 minutes. In some embodiments, the amplification reaction time is about 1 minute, about 3 minutes, about 5 minutes, about 7 minutes, about 10 minutes, about 13 minutes, about 15 minutes, about 17 minutes, about 20 minutes, about 25 minutes, about 30 minutes, or about 40 minutes. In some embodiments, the amplification reaction time is at least about 1 minute, about 3 minutes, about 5 minutes, about 7 minutes, about 10 minutes, about 13 minutes, about 15 minutes, about 17 minutes, about 20 minutes, about 25 minutes, or about 30 minutes. In some embodiments, the amplification reaction time is at most about 3 minutes, about 5 minutes, about 7 minutes, about 10 minutes, about 13 minutes, about 15 minutes, about 17 minutes, about 20 minutes, about 25 minutes, about 30 minutes, or about 40 minutes. [0081] In some embodiments, the amplification reaction time less than about 5 minutes to about 30 minutes. In some embodiments, the amplification reaction time less than about 5 minutes to about 7 minutes, about 5 minutes to about 10 minutes, about 5 minutes to about 13 minutes, about 5 minutes to about 15 minutes, about 5 minutes to about 17 minutes, about 5 minutes to about 20 minutes, about 5 minutes to about 25 minutes, about 5 minutes to about 30 minutes, about 7 minutes to about 10 minutes, about 7 minutes to about 13 minutes, about 7 minutes to about 15 minutes, about 7 minutes to about 17 minutes, about 7 minutes to about 20 minutes, about 7 minutes to about 25 minutes, about 7 minutes to about 30 minutes, about 10 minutes to about 13 minutes, about 10 minutes to about 15 minutes, about 10 minutes to about 17 minutes, about 10 minutes to about 20 minutes, about 10 minutes to about 25 minutes, about 10 minutes to about 30 minutes, about 13 minutes to about 15 minutes, about 13 minutes to about 17 minutes, about 13 minutes to about 20 minutes, about 13 minutes to about 25 minutes, about 13 minutes to about 30 minutes, about 15 minutes to about 17 minutes, about 15 minutes to about 20 minutes, about 15 minutes to about 25 minutes, about 15 minutes to about 30 minutes, about 17 minutes to about 20 minutes, about 17 minutes to about 25 minutes, about 17 minutes to about 30 minutes, about 20 minutes to about 25 minutes, about 20 minutes to about 30 minutes, or about 25 minutes to about 30 minutes. In some embodiments, the amplification reaction time less than about 5 minutes, about 7 minutes, about 10 minutes, about 13 minutes, about 15 minutes, about 17 minutes, about 20 minutes, about 25 minutes, or about 30 minutes. In some embodiments, the amplification reaction time less than at least about 5 minutes, about 7 minutes, about 10 minutes, about 13 minutes, about 15 minutes, about 17 minutes, about 20 minutes, or about 25 minutes. In some embodiments, the amplification reaction time less than at most about 7 minutes, about 10 minutes, about 13 minutes, about 15 minutes, about 17 minutes, about 20 minutes, about 25 minutes, or about 30 minutes. [0082] In some embodiments, amplifying reaction may be performed at a temperature of about 20 to about 45ºC. Amplifying may be performed at a temperature of less than about 20ºC, less than about 25ºC, less than about 30ºC, 35ºC, less than about 37ºC, less than about 40ºC, or less than about 45ºC. The nucleic acid amplification reaction may be performed at a temperature of at least about 20ºC, at least about 25ºC, at least about 30ºC, at least about 35ºC, at least about 37ºC, at least about 40ºC, or at least about 45ºC. b. Detection of Nucleic Acids [0083] Disclosed herein, in some instances, are methods of detecting the presence or absence of the target nucleic acid comprising the nucleotide variant at a position of interest, the method comprising: (a) contacting a sample to: (i) a composition comprising an effector protein and a guide nucleic acid; and (ii) a reporter comprising a nucleic acid and a detectable moiety, and (a) detecting the presence or absence of the target nucleic acid comprising the nucleotide variant by assaying for a signal, or change in signal, produced by trans cleavage of the reporter by the effector protein, wherein the trans cleavage is activated upon hybridization of the guide nucleic acid to the target nucleic acid molecule comprising the nucleotide variant; and (b) comparing the signal, or change in signal, to a control signal produced by contacting the composition and reporter to a control nucleic acid molecule not comprising the nucleotide variant, but that is (i) otherwise identical to the target nucleic acid molecule or (ii) otherwise identical to the target nucleic molecule apart from a variation of less than two nucleotides. In some embodiments, detecting the presence or absence of the target nucleic acid comprising the nucleotide variant at a position of interest in a sample, or a fraction thereof, comprises pre- amplification of the sample. In some embodiments, the pre-amplified sample comprises purified genomic sample, non-purified genomic sample, or any combination thereof. In some embodiments, detecting the presence or absence of the target nucleic acid comprises contacting the sample to the composition comprising the effector protein, the guide nucleic acid, and the reporter. In some embodiments, the effector protein is a Cas effector protein. In some embodiments, the effector protein is a Type V Cas effector protein, a Type VI Cas effector protein, a fraction thereof, or any combination thereof. In some embodiments, the effector protein is a type V Cas effector protein, or a fraction thereof. In some embodiments, the type V Cas effector protein is a Cas12 protein, or a fraction thereof. In some embodiments, the Cas12 protein comprises a Cas12a polypeptide, a Cas12b polypeptide, a Cas12c polypeptide, a Cas12d polypeptide, a Cas12e polypeptide, a C2c4 polypeptide, a C2c8 polypeptide, a C2c5 polypeptide, a C2c10 polypeptide, a C2c9 polypeptide, a Cas12f protein, a Cas12g protein, a Cas12h protein, a Cas12i protein, a Cas12j protein, a Cas12k protein, a fraction thereof, or any combination thereof. In some embodiments, the effector protein is a Cas14 protein, or a fraction thereof. In some embodiments, the Cas14 protein comprises a Cas14a polypeptide, a Cas14b polypeptide, a Cas14c polypeptide, a Cas14d polypeptide, a Cas14e polypeptide, a Cas14f polypeptide, a Cas14g polypeptide, a Cas14h polypeptide, a Cas14i polypeptide, a Cas14j polypeptide, a Cas14k polypeptide, a fraction thereof, or any combination thereof. In some embodiments, the effector protein is a CasФ protein, or fraction thereof. In some embodiments, the effector protein is a Cas13 protein, or a fraction thereof. In some embodiments, the Cas13 protein comprises a Cas13a polypeptide, a Cas13b polypeptide, a Cas13c polypeptide, a Cas13c polypeptide, a Cas13d polypeptide, a Cas13e polypeptide, a Cas13f polypeptide, a fraction thereof, or any combination thereof. In some embodiments, the Cas13 is at least one of LbuCas13a, LwaCas13a, LbaCas13a, HheCas13a, PprCas13a, EreCas13a, CamCas13a, or LshCas13a. In some embodiments, the composition comprises more than one effector protein. In some embodiments, the composition comprises more than one effector protein and/or more than one guide nucleic acid. In some embodiments, more than one effector protein and/or more than one guide nucleic acid is/are associated with more than one reporter. In some embodiments a single effector protein is associated with more than one guide nucleic acid. In some embodiments, a single effector protein is associated with more than one reporter. [0084] The effector proteins disclosed herein may exhibit trans cleavage activity upon activation. The trans cleavage activity of the effector protein can be activated when the gRNA is complexed with the target nucleic acid. The trans cleavage activity of the effector protein can be activated when the gRNA and the intermediary RNA are complexed with the target nucleic acid. The target nucleic acid can be a DNA, RNA, DNA reverse transcribed from RNA, RNA in vitro transcribed from DNA, or an amplicon of any of these. Preferably, the target nucleic acid is double stranded DNA. Thus, a Cas protein of the present disclosure can be activated by a target DNA to initiate trans cleavage activity of the Cas protein that cleaves a DNA reporter nucleic acid. For example, Cas proteins disclosed herein are activated by the binding of the gRNA to a target DNA that was reverse transcribed from an RNA to cleave nucleic acids of a reporter nucleic acid in a sequence-independent manner. For example, Cas proteins disclosed herein are activated by the binding of the gRNA to a target DNA that was amplified from a DNA to trans- collaterally cleave reporter nucleic acid molecules. The reporter nucleic acids can be DNA reporter nucleic acids (e.g., single stranded DNA coupled to detectable labels). In some embodiments, the Cas protein recognizes and detects double stranded DNA (dsDNA) and, further, trans cleaves single stranded DNA (ssDNA) reporter nucleic acids. Multiple Cas isolates can recognize, be activated by, and detect target DNA as described herein, including dsDNA. Therefore, an effector protein can be used to detect target DNA by assaying for cleaved DNA reporter nucleic acids. [0085] The cis cleavage activity of the effector protein can be activated when the gRNA is complexed with the target nucleic acid. The cis cleavage activity of the effector protein can be activated when the gRNA and the intermediary RNA are complexed with the target nucleic acid. The target nucleic acid can be a DNA, RNA, DNA reverse transcribed from RNA, RNA in vitro transcribed from DNA, or an amplicon of any of these. Preferably, the target nucleic acid is double stranded DNA. Thus, a Cas protein of the present disclosure can be activated by a target DNA to initiate cis cleavage activity of the Cas protein that cleaves the target DNA. For example, Cas proteins disclosed herein are activated by the binding of the gRNA to a target DNA that was amplified from a DNA to cleave the target DNA. In some embodiments, the sequence of the target DNA may be modified following cleavage of the target DNA. For example, an insertion sequence may be inserted at the site of cleavage of the target DNA. An insertion sequence may be a DNA sequence (e.g., a ssDNA sequence or a dsDNA sequence) or an RNA sequence. In another example, a segment of the target nucleic acid next to the site of cleavage may be removed from the target nucleic acid. In a further example, a segment of the target nucleic acid next to the site of cleavage may be replaced by an insertion sequence. [0086] In some embodiments, the effector protein may be present in the cleavage reaction at a concentration of about 10 nM, about 20 nM, about 30 nM, about 40 nM, about 50 nM, about 60 nM, about 70 nM, about 80 nM, about 90 nM, about 100 nM, about 200 nM, about 300 nM, about 400 nM, about 500 nM, about 600 nM, about 700 nM, about 800 nM, about 900 nM, about 1 µM, about 10 µM, or about 100 µM. In some embodiments, the effector protein may be present in the cleavage reaction at a concentration of from 10 nM to 20 nM, from 20 nM to 30 nM, from 30 nM to 40 nM, from 40 nM to 50 nM, from 50 nM to 60 nM, from 60 nM to 70 nM, from 70 nM to 80 nM, from 80 nM to 90 nM, from 90 nM to 100 nM, from 100 nM to 200 nM, from 200 nM to 300 nM, from 300 nM to 400 nM, from 400 nM to 500 nM, from 500 nM to 600 nM, from 600 nM to 700 nM, from 700 nM to 800 nM, from 800 nM to 900 nM, from 900 nM to 1 µM, from 1 µM to 10 µM, from 10 µM to 100 µM, from 10 nM to 100 nM, from 10 nM to 1 µM, from 10 nM to 10 µM, from 10 nM to 100 µM, from 100 nM to 1 µM, from 100 nM to 10 µM, from 100 nM to 100 µM, or from 1 µM to 100 µM. In some embodiments, the effector protein may be present in the cleavage reaction at a concentration of from 20 nM to 50 µM, from 50 nM to 20 µM, or from 200 nM to 5 µM. [0087] An effector protein can be used to detect or modify DNA at multiple pH values. An effector protein can be used to detect DNA at multiple pH values. A Cas protein that detects a target DNA can exhibit consistent cleavage across a wide range of pH conditions, such as from a pH of about 8.5 to a pH of about 9.0. In some embodiments, Cas DNA detection may exhibit high cleavage activity at pH values from 6 to 6.5, from 6.1 to 6.6, from 6.2 to 6.7, from 6.3 to 6.8, from 6.4 to 6.9, from 6.5 to 7, from 6.6 to 7.1, from 6.7 to 7.2, from 6.8 to 7.3, from 6.9 to 7.4, from 7 to 7.5, from 7.1 to 7.6, from 7.2 to 7.7, from 7.3 to 7.8, from 7.4 to 7.9, from 7.5 to 8, from 7.6 to 8.1, from 7.7 to 8.2, from 7.8 to 8.3, from 7.9 to 8.4, from 8 to 8.5, from 8.1 to 8.6, from 8.2 to 8.7, from 8.3 to 8.8, from 8.4 to 8.9, from 8.5 to 9, from 8.6 to 9.1, from 8.7 to 9.2, from 8.8 to 9.3, from 8.9 to 9.4, from 9 to 9.5, from 7 to 9, from 7.5 to 9, or from 8 to 9. For example, an effector protein may exhibit high cleavage at a pH of about 8.8. [0088] Target DNA detected by an effector protein complexed with a gRNA as disclosed herein can be directly obtained from organisms, or can be indirectly generated by nucleic acid amplification methods, such as PCR and LAMP of DNA, in vitro transcription of DNA, or reverse transcription of RNA. Key steps for the sensitive detection of direct DNA by an effector protein, e.g., a Cas, can include: (1) production or isolation of DNA to concentrations above about 0.1 nM per reaction for in vitro diagnostics, (2) selection of a target DNA with the appropriate sequence features to enable DNA detection as these some of these features are distinct from those required for target RNA detection, and (3) buffer composition that enhances DNA detection. The detection of DNA by an effector protein can be connected to a variety of readouts including fluorescence, lateral flow, electrochemistry, or any other readouts described herein. Methods for the generation of dsDNA for a DNA-activated programmable RNA nuclease-based detection or diagnostics can include (1) PCR, (2) isothermal amplification, such as RPA, LAMP, SDA, etc. (3) NEAR, and (4) conversion of RNA targets into dsDNA by a reverse transcriptase followed by RNase H digestion and PCR. Thus, an effector protein detection of target DNA is compatible with the various systems, kits, compositions, reagents, and methods disclosed herein. Cas DNA detection can be employed in a DETECTR assay disclosed herein to provide CRISPR diagnostics leveraging Type V system Cas for the detection of a target DNA. [0089] Some effector proteins can exhibit a high turnover rate. Turnover rate quantifies how many molecules of a reporter nucleic acid each effector protein is cleaving per minute. Effector proteins with a higher turnover rate are more efficient and transcollateral cleavage in the DETECTR assay methods disclosed herein. [0090] Turnover rate is quantified as the max transcleaving velocity (max slope in a plot of signal versus time in a DETECTR assay) divided by the amount of effector protein complexed with the gRNA present in the DETECTR assay, wherein the effector protein is at saturation with respect to its active site for transcollateral cleavage of reporter nucleic acids. [0091] Turnover rate can be quantified with the following equation:

[0092] Signal normalization factor is based on a standard curve and is the amount of signal produced from a known quantity of reporter nucleic acid (substrate of transcollateral cleavage). The turnover rate is, thus, expressed as cleaved reporter nucleic acid molecules per minute divided by the concentration of the effector protein complexed with an engineered guide RNA system (can also be referred to as “nucleoprotein” or “ribonucleoprotein”). Therefore, an effector protein with a high turnover rate exhibits superior and highly efficient transcollateral cleavage of reporter nucleic acids in the DETECTR assay methods disclosed herein. For example, an effector protein that recognizes a PAM of TR, wherein R is A or G, complexed with an egRNA system comprises a turnover rate of at least about 0.01 cleaved reporter molecules per minute per effector protein. The effector protein may be a Type V effector protein. The effector protein may be a Cas12 effector protein. [0093] In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.01 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.05 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.06 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.07 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.08 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.09 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.1 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.11 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.12 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.13 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.14 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.15 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.16 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.17 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.18 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.19 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.20 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.22 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.24 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.26 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.28 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.3 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.4 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.5 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.01 to 0.5 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.01 to 0.2 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.01 to 0.05 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.05 to 0.10 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.10 to 0.15 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.15 to 0.20 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.20 to 0.25 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.25 to 0.30 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.30 to 0.35 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.35 to 0.40 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.40 to 0.45 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.45 to 0.50 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.01 to 1 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.01 to 0.2 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.01 to 0.3 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.01 to 0.4 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.1 to 0.3 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.2 to 0.4 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.3 to 0.5 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.4 to 0.6 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.5 to 0.7 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.6 to 0.8 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.7 to 0.9 cleaved reporter molecules per minute per effector protein. In some embodiments, effector proteins with a high turnover rate have a turnover rate of at least about 0.8 to 1.0 cleaved reporter molecules per minute per effector protein. [0094] In some cases, the methods, compositions, reagents, enzymes, and kits described herein may be used to detect a target single-stranded nucleic acid in a sample where the sample is contacted with the reagents for a predetermined length of time sufficient for the trans cleavage to occur or cleavage reaction to reach completion. In some cases, the devices, systems, fluidic devices, kits, and methods described herein detect a target single-stranded nucleic acid in a sample where the sample is contacted with the reagents for no greater than 60 minutes. Sometimes the sample is contacted with the reagents for no greater than 120 minutes, 110 minutes, 100 minutes, 90 minutes, 80 minutes, 70 minutes, 60 minutes, 55 minutes, 50 minutes, 45 minutes, 40 minutes, 35 minutes, 30 minutes, 25 minutes, 20 minutes, 15 minutes, 10 minutes, 5 minutes, 4 minutes, 3 minutes, 2 minutes, or 1 minute. Sometimes the sample is contacted with the reagents for at least 120 minutes, 110 minutes, 100 minutes, 90 minutes, 80 minutes, 70 minutes, 60 minutes, 55 minutes, 50 minutes, 45 minutes, 40 minutes, 35 minutes, 30 minutes, 25 minutes, 20 minutes, 15 minutes, 10 minutes, or 5 minutes. In some cases, the sample is contacted with the reagents for from 5 minutes to 120 minutes, from 5 minutes to 100 minutes, from 10 minutes to 90 minutes, from 15 minutes to 45 minutes, or from 20 minutes to 35 minutes. In some cases, the devices, systems, fluidic devices, kits, and methods described herein can detect a target nucleic acid in a sample in less than 10 hours, less than 9 hours, less than 8 hours, less than 7 hours, less than 6 hours, less than 5 hours, less than 4 hours, less than 3 hours, less than 2 hours, less than 1 hour, less than 50 minutes, less than 45 minutes, less than 40 minutes, less than 35 minutes, less than 30 minutes, less than 25 minutes, less than 20 minutes, less than 15 minutes, less than 10 minutes, less than 9 minutes, less than 8 minutes, less than 7 minutes, less than 6 minutes, or less than 5 minutes. In some cases, the devices, systems, fluidic devices, kits, and methods described herein can detect a target nucleic acid in a sample in from 5 minutes to 10 hours, from 10 minutes to 8 hours, from 15 minutes to 6 hours, from 20 minutes to 5 hours, from 30 minutes to 2 hours, or from 45 minutes to 1 hour. [0095] When a gRNA binds to a target nucleic acid, the effector protein’s trans cleavage activity can be initiated, and nucleic acids of a reporter nucleic acid can be cleaved, resulting in the detection of fluorescence. The gRNA may be a non-naturally occurring gRNA. A non- naturally occurring gRNA may comprise an engineered sequence having a repeat and a spacer that hybridizes to a target nucleic acid sequence of interest. A non-naturally occurring gRNA may be recombinantly expressed or chemically synthezised. Nucleic acid reporter nucleic acids can comprise a detection moiety, wherein the nucleic acid reporter nucleic acid can be cleaved by the activated effector protein, thereby generating a signal. Some methods as described herein can a method of assaying for a target nucleic acid in a sample comprises contacting the sample to a complex comprising a gRNA comprising a segment that is reverse complementary to a segment of the target nucleic acid and an effector protein that exhibits sequence independent cleavage upon forming a complex comprising the segment of the gRNA binding to the segment of the target nucleic acid; and assaying for a signal indicating cleavage of at least some protein- nucleic acids of a population of protein-nucleic acids, wherein the signal indicates a presence of the target nucleic acid in the sample and wherein absence of the signal indicates an absence of the target nucleic acid in the sample. The cleaving of the nucleic acid of a reporter nucleic acid using the effector protein may cleave with an efficiency of 50% as measured by a change in a signal that is calorimetric, potentiometric, amperometric, optical (e.g., fluorescent, colorimetric, etc.), or piezo-electric, as non-limiting examples. Some methods as described herein can be a method of detecting a target nucleic acid in a sample comprising contacting the sample comprising the target nucleic acid with a gRNA targeting a target nucleic acid segment, an effector protein capable of being activated when complexed with the gRNA and the target nucleic acid segment, a single stranded nucleic acid of a reporter nucleic acid comprising a detection moiety, wherein the nucleic acid of a reporter nucleic acid is capable of being cleaved by the activated effector protein, thereby generating a first detectable signal, cleaving the single stranded nucleic acid of a reporter nucleic acid using the effector protein that cleaves as measured by a change in color, and measuring the first detectable signal on the support medium. The cleaving of the single stranded nucleic acid of a reporter nucleic acid using the effector protein may cleave with an efficiency of 50% as measured by a change in color. In some cases, the cleavage efficiency is at least 40%, 50%, 60%, 70%, 80%, 90%, or 95% as measured by a change in color. The change in color may be a detectable colorimetric signal or a signal visible by eye. The change in color may be measured as a first detectable signal. The first detectable signal can be detectable within 5 minutes of contacting the sample comprising the target nucleic acid with a gRNA targeting a target nucleic acid segment, an effector protein capable of being activated when complexed with the gRNA and the target nucleic acid segment, and a single stranded nucleic acid of a reporter nucleic acid comprising a detection moiety, wherein the nucleic acid of a reporter nucleic acid is capable of being cleaved by the activated nuclease. The first detectable signal can be detectable within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 70, 80, 90, 100, 110, or 120 minutes of contacting the sample. In some embodiments, the first detectable signal can be detectable within from 1 to 120, from 5 to 100, from 10 to 90, from 15 to 80, from 20 to 60, or from 30 to 45 minutes of contacting the sample. [0096] In some cases, the methods, reagents, enzymes, and kits described herein detect a target single-stranded nucleic acid with an effector protein and a single-stranded nucleic acid of a reporter nucleic acid in a sample where the sample is contacted with the reagents for a predetermined length of time sufficient for trans cleavage of the single stranded nucleic acid of a reporter nucleic acid. In a preferred embodiment, a Cas protein may be used to detect the presence of a single-stranded DNA target nucleic acid. For example, an effector protein is Cas protein that detects a target nucleic acid and a single stranded nucleic acid of a reporter nucleic acid with a green detectable moiety that is detected upon cleavage. As another example, an effector protein is Cas protein that detects a target nucleic acid and a single-stranded nucleic acid of a reporter nucleic acid with a red detectable moiety that is detected upon cleavage. III. Effector Proteins [0097] Disclosed herein are effector proteins and uses thereof, e.g., detection of target nucleic acids. In some instances, effector proteins comprise a Type V CRISPR/Cas protein. In some instances, Type V CRISPR/Cas proteins comprise nucleic acid cleavage activity. In some instances, Type V CRISPR/Cas proteins cleave or nick single-stranded nucleic acids, double, stranded nucleic acids, or a combination thereof. In some cases, Type V CRISPR/Cas proteins cleave single-stranded nucleic acids. In some cases, Type V CRISPR/Cas proteins cleave double-stranded nucleic acids. In some cases, Type V CRISPR/Cas proteins nick double- stranded nucleic acids. Typically, guide RNAs of Type V CRISPR/Cas proteins hybridize to ssDNA or dsDNA. However, the trans cleavage activity of Type V CRISPR/Cas protein is typically directed towards ssDNA. [0098] In some cases, the Type V CRISPR/Cas protein comprises a catalytically inactive nuclease domain. In some cases, the Type V CRISPR/Cas protein comprises a catalytically inactive nuclease domain. A catalytically inactive domain of a Type V CRISPR/Cas protein may comprise at least 1, at least 2, at least 3, at least 4, or at least 5 mutations relative to a wild type nuclease domain of the Type V CRISPR/Cas protein. Said mutations may be present within a cleaving or active site of the nuclease. [0099] The Type V CRISPR/Cas protein may be a Cas14 protein. The Type V CRISPR/Cas protein may be a Cas12 protein. The Type V CRISPR/Cas protein may be a CasФ protein. The Type V CRISPR/Cas protein may be a CasY protein. [0100] In some instances, the Type V CRISPR/Cas protein has been modified (also referred to as an engineered protein). In some instances, an engineered protein comprises an amino acid sequence that is at 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 92%, at least 95%, at least 97%, at least 99%, or 100% identical to any one of SEQ ID NOS: 1- 208. A Type V CRISPR/Cas protein disclosed herein or a variant thereof may comprise a nuclear localization signal (NLS). In some cases, the NLS may comprise a sequence of KRPAATKKAGQAKKKKEF. Type V CRISPR/Cas proteins may be codon optimized for expression in a specific cell, for example, a bacterial cell, a plant cell, a eukaryotic cell, an animal cell, a mammalian cell, or a human cell. In some embodiments, the Type V CRISPR/Cas protein is codon optimized for a human cell. [0101] In some cases, compositions comprise a Type V CRISPR/Cas protein and a cell. In some embodiments, compositions comprise a cell that expresses a Type V CRISPR/Cas protein. In some cases, compositions comprise a nucleic acid encoding a Type V CRISPR/Cas protein and a cell. In some embodiments, compositions comprise a cell expressing a nucleic acid encoding a Type V CRISPR/Cas protein. In some instances, the cell is a prokaryotic cell. In some instances, the cell is a eukaryotic cell. In some instances, the cell is a mammalian cell. Cas12 [0102] In some embodiments, the Type V CRISPR/Cas protein is a Cas12 protein. Type V CRISPR/Cas proteins (e.g., Cas12) lack an HNH domain. A Cas12 nuclease of the present disclosure cleaves a nucleic acid via a single catalytic RuvC domain. This single catalytic RuvC domain includes 3 partial RuvC domains (RuvC-I, RuvC-II, and RuvC-III, also referred to herein as subdomains) that are not contiguous with respect to the primary amino acid sequence of the Cas12 protein, but form an RuvC domain once the protein is produced and folds. In some embodiments, an effector protein comprises three partial RuvC domains. In some embodiments, an effector protein comprises an RuvC-I subdomain, an RuvC-II subdomain, and an RuvC-III subdomain. The RuvC domain is within a nuclease, or “NUC” lobe of the protein, and the Cas12 nucleases further comprise a recognition, or “REC” lobe. The REC and NUC lobes are connected by a bridge helix and the Cas12 proteins additionally include two domains for PAM recognition termed the PAM interacting (PI) domain and the wedge (WED) domain. (Murugan et al., Mol Cell.2017 Oct 5; 68(1): 15–25). [0103] In some embodiments, a Cas12 protein may recognize a PAM having a sequence of TR, where R represents any purine (e.g., A or G). In some embodiments, a Cas12 protein may recognize a PAM having a sequence of TN, where N represents any nucleotide (e.g., A, C, T, U, or G). In some embodiments, a Cas12 protein may recognize a PAM having a sequence of TA. In some embodiments, a Cas12 protein may recognize a PAM having a sequence of TG. [0104] In some instances, a Cas12 protein. The Cas12 protein may be a Cas12a protein (also referred to as Cpf1), a Cas12b protein, Cas12c protein, Cas12d protein, a Cas12e protein, a Cas12e protein, a Cas12f protein, a Cas12g protein, a Cas12h protein, a Cas12i protein, a Cas12j protein, or a Cas12k protein. The Cas12c protein may be a C12c4 protein, a C12c8 protein, a C12c5 protein, a C12c10 protein, or a C12c9 protein. [0105] In some cases, the Cas12 protein is capable of cleaving a nucleic acid via a single catalytic RuvC domain. In such cases, the Cas12 protein may cleave both strands of a double- stranded target nucleic acid molecule within the single catalytic RuvC domain. The RuvC domain may be disposed within a nuclease lobe (NUC lobe) of the protein. The RuvC domain may target complementary positions on a double stranded nucleic acid target, or may target separate positions (e.g., between different base pairs) on the target and non-target strands of the target nucleic acid. [0106] A Cas12 protein may comprise a recognition lobe (REC lobe) which may have a binding affinity for a guide nucleic acid or for a guide nucleic acid-target nucleic acid complex. In some cases, a REC lobe comprises a binding affinity for a PAM sequence in the target nucleic acid. Some Cas12 proteins (e.g., SEQ ID NO: 1) comprise two recognition domains, which may both be disposed within the REC lobe. The two recognition domains may separately identify and direct nuclease binding to PAM sequences disposed within separate strands of the target nucleic acid. The REC lobe may be disposed between regions of a wedge (WED) domain. The REC lobe may be connected to the NUC lobe by a bridge helix. A Cas12 protein may additionally include two domains for PAM recognition termed the PAM interacting (PI) domain and the wedge (WED) domain. [0107] In some cases, the effector proteins comprise a Cas12 protein, wherein the amino acid sequence of the Cas12 protein comprises an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to any one of SEQ ID NOs: 1-43, as provided in TABLE 1. In some cases, the amino acid sequence of the Cas 12 protein consists of an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to any one of SEQ ID NOs: 1-43. [0108] In some embodiments, the method of the disclosure uses an effector protein of the present disclosure which comprises a sequences from a Cas12 variant or ortholog. In some embodiments, the effector protein comprises an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to any one of SEQ ID NO: 11. CasФ [0109] In some instances, the method comprises the use of an effector protein comprising a CasФ protein (also referred to as CasPhi). A CasФ protein may function as an endonuclease that catalyzes cleavage at a specific sequence in a target nucleic acid. A CasФ protein may have a compact catalytic site in a RuvC domain that is capable of catalyzing pre-gRNA processing and nicking or cleaving of nucleic acids. The compact catalytic site may render the CasФ protein especially advantageous for genome engineering and new functionalities for genome manipulation. A CasФ protein may also be referred to as a Cas12J protein. [0110] A CasФ protein may have a molecular weight of about 65 kiloDaltons (kDa) to about 85 kDa. For example, a CasФ protein can have a molecular weight of about 65 kDa to about 70 kDa, about 70 kDa to about 75 kDa, or about 75 kDa to about 80 kDa. For example, a CasФ protein may have a molecular weight of from about 70 kDa to about 80 kDa. [0111] In some instances, effector protein comprise a CasФ protein, wherein the amino acid sequence of the CasФ protein comprises an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to any one of SEQ ID NOs: 44-91, as provided in TABLE 1 below. In some cases, the amino acid sequence of the CasФ protein consists of an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to any one of SEQ ID NOs: 44-91. TABLE 1 – Cas12 and CasФ Effector Protein Sequences

Cas14 Effector Proteins [0112] Disclosed herein are effector proteins and uses thereof, e.g., detection and editing of target nucleic acids using Cas14 effector proteins. [0113] In some instances, the effector protein comprises a Cas14 protein. Cas14 proteins may comprise a bilobed structure with distinct amino-terminal and carboxy-terminal domains. The amino- and carboxy-terminal domains may be connected by a flexible linker. The flexible linker may affect the relative conformations of the amino- and carboxyl-terminal domains. The flexible linker may be short, for example less than 10 amino acids, less than 8 amino acids, less than 6 amino acids, less than 5 amino acids, or less than 4 amino acids in length. The flexible linker may be sufficiently long to enable different conformations of the amino- and carboxy- terminal domains among two Cas14 proteins of a Cas14 dimer complex (e.g., the relative orientations of the amino- and carboxy-terminal domains differ between two Cas14 proteins of a Cas14 homodimer complex). The linker domain may comprise a mutation which affects the relative conformations of the amino- and carboxyl-terminal domains. The linker may comprise a mutation which affects Cas14 dimerization. For example, a linker mutation may enhance the stability of a Cas14 dimer. [0114] In some instances, the amino-terminal domain of a Cas14 protein comprises a wedge domain, a recognition domain, a zinc finger domain, or any combination thereof. The wedge domain may comprise a multi-strand β-barrel structure. A multi-strand β-barrel structure may comprise an oligonucleotide/oligosaccharide-binding fold that is structurally comparable to those of some Cas12 proteins. The recognition domain and the zinc finger domain may each (individually or collectively) be inserted between β-barrel strands of the wedge domain. The recognition domain may comprise a 4-α-helix structure, structurally comparable but shorter than those found in some Cas12 proteins. The recognition domain may comprise a binding affinity for a guide nucleic acid or for a guide nucleic acid-target nucleic acid heteroduplex. In some cases, a REC lobe may comprise a binding affinity for a PAM sequence in the target nucleic acid. The amino-terminal may comprise a wedge domain, a recognition domain, and a zinc finger domain. The carboxy-terminal may comprise a RuvC domain, a zinc finger domain, or any combination thereof. The carboxy-terminal may comprise one RuvC and one zinc finger domain. [0115] Cas14 proteins may comprise a RuvC domain or a partial RuvC domain. The RuvC domain may be defined by a single, contiguous sequence, or a set of partial RuvC domains that are not contiguous with respect to the primary amino acid sequence of the Cas14 protein. In some instances, a partial RuvC domain does not have any substrate binding activity or catalytic activity on its own. A Cas14 protein of the present disclosure may include multiple partial RuvC domains, which may combine to generate a RuvC domain with substrate binding or catalytic activity. For example, a Cas14 may include 3 partial RuvC domains (RuvC-I, RuvC-II, and RuvC-III, also referred to herein as subdomains) that are not contiguous with respect to the primary amino acid sequence of the Cas14 protein, but form a RuvC domain once the protein is produced and folds. A Cas14 protein may comprise a linker loop connecting a carboxy terminal domain of the Cas14 protein with the amino terminal domain of the Cas 14 protein, and wherein the carboxy terminal domain comprises one or more RuvC domains and the amino terminal domain comprises a recognition domain. [0116] Cas14 proteins may comprise a zinc finger domain. In some instances, a carboxy terminal domain of a Cas14 protein comprises a zinc finger domain. In some instances, an amino terminal domain of a Cas14 protein comprises a zinc finger domain. In some instances, the amino terminal domain comprises a wedge domain (e.g., a multi-β-barrel wedge structure), a zinc finger domain, or any combination thereof. In some cases, the carboxy terminal domain comprises the RuvC domains and a zinc finger domain, and the amino terminal domain comprises a recognition domain, a wedge domain, and a zinc finger domain. [0117] Cas14 proteins may be relatively small compared to many other Cas proteins, making them suitable for nucleic acid detection or gene editing. For instance, a Cas14 protein may be less likely to adsorb to a surface or another biological species due to its small size. The smaller nature of these proteins also allows for them to be more easily packaged as a reagent in a system or assay, and delivered with higher efficiency as compared to other larger Cas proteins. In some cases, a Cas14 protein is 400 to 800 amino acid residues long, 400 to 600 amino acid residues long, 440 to 580 amino acid residues long, 460 to 560 amino acid residues long, 460 to 540 amino acid residues long, 460 to 500 amino acid residues long, 400 to 500 amino acid residues long, or 500 to 600 amino acid residues long. In some cases, a Cas14 protein is less than about 550 amino acid residues long. In some cases, a Cas14 protein is less than about 500 amino acid residues long. [0118] In some instances, a Cas14 protein may function as an endonuclease that catalyzes cleavage at a specific position within a target nucleic acid. In some instances, a Cas14 protein is capable of catalyzing non-sequence-specific cleavage of a single stranded nucleic acid. In some cases, a Cas14 protein is activated to perform trans cleavage activity after binding of a guide nucleic acid with a target nucleic acid. This trans cleavage activity is also referred to as “collateral” or “trans-collateral” cleavage. Trans cleavage activity may be non-specific cleavage of nearby single-stranded nucleic acid by the activated effector protein, such as trans cleavage of reporter nucleic acids with a detection moiety. [0119] A Cas14 protein may comprise an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to any one of SEQ ID NOs: 92-96. SEQ ID NOs: 92-96 are provided in Table 2. In some cases, the amino acid sequence of the Cas14 protein is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or at least 98%, at least 99%, or 100% identical to any one of SEQ ID NOs: 92-96. The amino acid sequence of the Cas14 protein may be at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or at least 98%, at least 99%, or 100% identical to SEQ ID NO: 92. The amino acid sequence of the Cas14 protein may be at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or at least 98%, at least 99%, or 100% identical to SEQ ID NO: 93. The amino acid sequence of the Cas14 protein may be at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or at least 98%, at least 99%, or 100% identical to SEQ ID NO: 94. The amino acid sequence of the Cas14 protein may be at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or at least 98%, at least 99%, or 100% identical to SEQ ID NO: 95. The amino acid sequence of the Cas14 protein may be at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or at least 98%, at least 99%, or 100% identical to SEQ ID NO: 96. In some instances, the multimeric complex comprises a first Cas14 protein and the second Cas14 protein each comprising an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% amino acid sequence identical to any one of SEQ ID NOs: 92-96. In some cases, each of the amino acid sequences of the first and second Cas14 proteins is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or 100% identical to any one of SEQ ID NOs: 92-188. [0120] In some cases, multimeric complexes comprise at least one Cas14 protein selected from a Cas14a protein, a Cas14b protein, a Cas14c protein, a Cas14d protein, a Cas14e protein, a Cas14f protein, a Cas14g protein, a Cas14h protein, and a Cas14u protein, and a combination thereof. In some cases, the amino acid sequence of the at least one Cas14 protein is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or 100% identical to any one of SEQ ID NOs: 97-188. [0121] In some instances, the amino acid sequence of the first Cas14 protein is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or 100% identical to any one of SEQ ID NOs: 92-96 and the second Cas14 protein is selected from a Cas14a protein, a Cas14b protein, a Cas14c protein, a Cas14d protein, a Cas14e protein, a Cas14f protein, a Cas14g protein, a Cas14h protein, and a Cas14u protein. In some cases, the amino acid sequence of the second Cas14 protein comprises an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to any one of SEQ ID NOs: 97-188, as provided in TABLE 2 below. In some cases, the amino acid sequence of the second Cas 14 protein consists of an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to any one of SEQ ID NOs: 97-188. [0122] The Type V CRISPR/Cas protein may be a Cas14 protein. The Cas 14 protein may be a Cas14a.1 protein. The Cas14a.1 protein may be represented by a sequence selected from the group consisting of SEQ ID NOs.92-126, or any sequence found in Table 2. The Cas14 protein may comprise an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to SEQ ID NOs.92-126, or any sequence found in Table 2. The Cas14 protein may consist of an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to SEQ ID NOs.92-126. [0123] The Type V CRISPR/Cas protein may be a Cas14 protein. The Cas 14 protein may be a Cas14a.1 protein. The Cas14a.1 protein may be represented by SEQ ID NO: 94, presented in Table 2. The Cas14 protein may comprise an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to SEQ ID NO: 94. The Cas14 protein may consist of an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to SEQ ID NO: 94. The Cas14 protein may comprise at least about 50, at least about 100, at least about 150, at least about 200, at least about 250, at least about 300, at least about 350, at least about 400, at least about 450, at least about 500 consecutive amino acids of SEQ ID NO: 94. Cas14 Dimers [0124] In some instances, the multimeric complex is a dimer comprising two Cas14 proteins, (also referred to as a “Cas14 dimer”), wherein the amino acid sequence of the first Cas14 protein is at least 90%, at least 92%, at least 94%, at least 96%, at least 98%, at least 99%, or 100% identical to the second Cas14 protein. In some instances, dimerization promotes Cas14 activity and/or substrate or guide nucleic acid binding. A Cas14 dimer may comprise a two-lobe structure with a central channel. The Cas14 dimer may comprise enhanced activity (e.g., binding affinity or target nucleic acid cleavage kinetics) relative to a Cas14 protein of the dimer in its monomeric form. The Cas14 dimer may bind a single guide nucleic acid and single target nucleic acid. The Cas14 dimer may be capable of performing one or both of cis-cleavage activity and transcollateral cleavage activity. [0125] In some instances, dimers comprise: a first Cas14 protein comprising at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 92%, at least 95%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to SEQ ID NO: 92 and a second Cas14 comprising at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 92%, at least 95%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to SEQ ID NO: 92. [0126] In some instances, dimers comprise: a first Cas14 protein comprising at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 92%, at least 95%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to SEQ ID NO: 93 and a second Cas14 comprising at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 92%, at least 95%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to SEQ ID NO: 93. [0127] In some instances, dimers comprise: a first Cas14 protein comprising at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 92%, at least 95%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to SEQ ID NO: 94 and a second Cas14 comprising at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 92%, at least 95%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to SEQ ID NO: 94. [0128] In some instances, dimers comprise: a first Cas14 protein comprising at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 92%, at least 95%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to SEQ ID NO: 95 and a second Cas14 comprising at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 92%, at least 95%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to SEQ ID NO: 95. [0129] In some instances, dimers comprise: a first Cas14 protein comprising at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 92%, at least 95%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to SEQ ID NO: 96 and a second Cas14 comprising at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 92%, at least 95%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to SEQ ID NO: 96. [0130] A Cas14 dimer may require specific conditions (e.g., a minimum ionic strength requirement) or a substrate or cofactor (e.g., a guide nucleic acid) for dimerization. A composition of the present disclosure may therefore comprise monomeric Cas14 proteins which dimerize upon modification of a solution condition (e.g., an increase in salinity or decrease in pH) or addition of a guide nucleic acid. A Cas14 protein of the present disclosure may exhibit concentration-dependent dimerization. For example, a Cas14 protein may comprise an equilibrium constant for dimerization (e.g., in standard conditions of at

least 0.0001 mM^-1, at least 0.0005 mM^-1, at least 0.001 mM^-1, at least 0.005 mM^-1, at least 0.01 mM^-1, at least 0.05 mM^-1, at least 0.1 mM^-1, at least 0.5 mM^-1, at least 1 mM^-1, at least 5 mM^-1, at least 10 mM^-1, at least 50 mM^-1, or at least 100 mM^-1. A Cas14 protein may comprise an equilibrium constant for dimerization that is less than about 50 mM^-1, less than about 10 mM^-1, less than about 5 mM^-1, less than about 1 mM^-1, less than about 0.5 mM^-1, less than about 0.1 mM^-1, less than about 0.05 mM^-1, less than about 0.01 mM^-1, less than about 0.005 mM^-1, less than about 0.001 mM^-1, less than about 0.0005 mM^-1, or less than about 0.0001 mM^-1. TABLE 2 – Cas14 effector Protein Sequences

CasY Effector Proteins [0131] Disclosed herein are effector proteins and uses thereof, e.g., detection and editing of target nucleic acids using CasY effector proteins. [0132] A CasY effector protein may include an N-terminal domain roughly 800-1000 amino acids in length (e.g., about 815 or about 980), and a C-terminal domain that includes 3 partial RuvC domains (RuvC-I, RuvC-II, and RuvC-III, also referred to herein as subdomains) that are not contiguous with respect to the primary amino acid sequence of the CasY protein, but form a RuvC domain once the protein is produced and folds. Thus, in some cases, a CasY protein (of the subject compositions and/or methods) includes an amino acid sequence with an N-terminal domain (e.g., not including any fused heterologous sequence such as a localization sequence and/or a domain with a catalytic activity) having a length in a range of from 750 to 1050 amino acids (e.g., from 750 to 1025, 750 to 1000, 750 to 950, 775 to 1050, 775 to 1025, 775 to 1000, 775 to 950, 800 to 1050, 800 to 1025, 800 to 1000, or 800 to 950 amino acids). In some cases, a CasY protein (of the subject compositions and/or methods) includes an amino acid sequence having a length (e.g., not including any fused heterologous sequence such as a localization sequence and/or a domain with a catalytic activity) in a range of from 750 to 1050 amino acids (e.g., from 750 to 1025, 750 to 1000, 750 to 950, 775 to 1050, 775 to 1025, 775 to 1000, 775 to 950, 800 to 1050, 800 to 1025, 800 to 1000, or 800 to 950 amino acids) that is N- terminal to a split Ruv C domain (e.g., 3 partial RuvC domains—RuvC-I, RuvC-II, and RuvC- III). [0133] In some cases, a CasY protein may recognize a protospacer adjacent motif (PAM) having a sequence of TR, where R represents any purine (e.g., A or G). In some embodiments, a CasY protein may recognize a PAM having a sequence of TN, where N represents any nucleotide (e.g., A, C, T, U, or G). In some embodiments, a CasY protein may recognize a PAM having a sequence of TA. In some embodiments, a CasY protein may recognize a PAM having a sequence of TG. A CasY protein can be a CasY variant. [0134] In some instances, the Cas14 protein comprises an amino acid sequence of the Cas14 protein is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to any one of SEQ ID NOs: 189-208, or any sequence found in Table 3. TABLE 3 – CasY Protein Sequences

Cas13 Effector Proteins [0135] In some embodiments, the Type VI CRISPR/Cas enzyme is a programmable Cas13 nuclease. The general architecture of a Cas13 protein includes an N-terminal domain and two HEPN (higher eukaryotes and prokaryotes nucleotide-binding) domains separated by two helical domains (Liu et al., Cell 2017 Jan 12;168(l-2):121-134.el2). The HEPN domains each comprise aR-X4-H motif. Shared features across Cas13 proteins include that upon binding of the crRNA of the guide nucleic acid guide nucleic acid to a target nucleic acid or segment thereof, the protein undergoes a conformational change to bring together the HEPN domains and form a catalytically active RNase. (Tambe et al., Cell Rep.2018 Jul 24; 24(4): 1025–1036.). Thus, two activatable HEPN domains are characteristic of a programmable Cas13 nuclease of the present disclosure. However, programmable Cas13 nucleases also consistent with the present disclosure include Cas13 nucleases comprising mutations in the HEPN domain that enhance the Cas13 proteins cleavage efficiency or mutations that catalytically inactivate the HEPN domains. [0136] A programmable Cas13 nuclease can be a Cas13a protein (also referred to as “c2c2”), a Cas13b protein, a Cas13c protein, a Cas13d protein, a Cas13e protein, or a Cas13f protein. Example C2c2 proteins are set forth as SEQ ID NOs: 392-409, provided in the Table 9 below. In some cases, a subject C2c2 protein includes an amino acid sequence having 80% or more (e.g., 85% or more, 90% or more, 95% or more, 98% or more, 99% or more, 99.5% or more, or 100%) amino acid sequence identity with the amino acid sequence set forth in any one of SEQ ID NOs: 392-409, provided in Table 9 below. TABLE 9 – Cas13 Protein Sequences

Additional Effector Proteins [0137] Table 10 provides additional illustrative amino acid sequences of programmable nucleases having trans-cleavage activity. In some instances, programmable nucleases described herein comprise an amino acid sequence that is at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or at least 98%, at least 99%, or 100% identical to any one of SEQ ID Nos: 410-443. The programmable nuclease may consist of an amino acid sequence that is at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to any one or SEQ ID Nos: 410-443. The programmable nuclease may comprise at least about 50, at least about 100, at least about 150, at least about 200, at least about 250, at least about 300, at least about 350, at least about 400, at least about 450, at least about 500 consecutive amino acids of any one of SEQ ID NOs: 410-443. In some embodiments, the programmable nuclease comprises the amino acid sequence of any one of SEQ ID NOs: 410-443. TABLE 10 – Further Cas Protein Sequences

Engineered Proteins [0138] In some instances, an effector protein disclosed herein is an engineered protein. The engineered protein is not identical to a naturally-occurring protein. The engineered protein may provide enhanced nuclease or nickase activity as compared to a naturally occurring nuclease or nickase. By way of non-limiting example, some engineered proteins exhibit optimal activity at lower salinity and viscosity than the protoplasm of their bacterial cell of origin. Also by way of non-limiting example, bacteria often comprise protoplasmic salt concentrations greater than 250 mM and room temperature intracellular viscosities above 2 centipoise, whereas engineered proteins exhibit optimal activity (e.g., cis-cleavage activity) at salt concentrations below 150 mM and viscosities below 1.5 centipoise. The present disclosure leverages these dependencies by providing engineered proteins in solutions optimized for their activity and stability. [0139] An engineered protein may comprise a modified form of a wild type counterpart protein. The modified form of the wild type counterpart may comprise an amino acid change (e.g., deletion, insertion, or substitution) that reduces the nucleic acid-cleaving activity of the effector protein. For example, a nuclease domain (e.g., RuvC domain) of a Type V CRISPR/Cas protein may be deleted or mutated so that it is no longer functional or comprises reduced nuclease activity. The modified form of the effector protein may have less than 90%, less than 80%, less than 70%, less than 60%, less than 50%, less than 40%, less than 30%, less than 20%, less than 10%, less than 5%, or less than 1% of the nucleic acid-cleaving activity of the wild-type counterpart. Engineered proteins may have no substantial nucleic acid-cleaving activity. Engineered proteins may be enzymatically inactive or “dead,” that is it may bind to a nucleic acid but not cleave it. An enzymatically inactive protein may comprise an enzymatically inactive domain (e.g. inactive nuclease domain). Enzymatically inactive may refer to an activity less than 1%, less than 2%, less than 3%, less than 4%, less than 5%, less than 6%, less than 7%, less than 8%, less than 9%, or less than 10% activity compared to the wild-type counterpart. A dead protein may associate with a guide nucleic acid to activate or repress transcription of a target nucleic acid sequence. In some embodiments, the enzymatically inactive protein is fused with a protein comprising recombinase activity. Fusion Proteins [0140] In some instances, an effector protein is a fusion protein, wherein the fusion protein comprises an effector protein of the present disclosure (e.g., a Cas12 effector protein) and a fusion partner protein. In some instances, the effector protein comprises an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or 100% identical to any one of the sequences found in Tables 1 -4. In some embodiments, the effector protein comprises at least70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or 100% sequence identity to SEQ ID NO: 11. [0141] A fusion partner protein is also simply referred to herein as a fusion partner. In some cases, the fusion partner promotes the formation of a multimeric complex of the effector protein. In some instances, the fusion partner inhibits the formation of a multimeric complex of the effector protein. By way of non-limiting example, the fusion protein may comprise a Cas12 protein, and a fusion partner comprising a Calcineurin A tag, wherein the fusion protein dimerizes in the presence of Tacrolimus (FK506). Also by way of non-limiting example, the fusion protein may comprise a Cas12 protein and a SpyTag configured to dimerize or associate with another effector protein in a multimeric complex. [0142] In some cases, fusion partners provide enzymatic activity that modifies a target nucleic acid. Such enzymatic activities include, but are not limited to, nuclease activity, methyltransferase activity, demethylase activity, DNA repair activity, DNA damage activity, deamination activity, dismutase activity, alkylation activity, depurination activity, oxidation activity, pyrimidine dimer forming activity, integrase activity, transposase activity, recombinase activity, polymerase activity, ligase activity, helicase activity, photolyase activity, and glycosylase activity. [0143] In some cases, a fusion partner provides enzymatic activity that modifies a protein (e.g., a histone) associated with a target nucleic acid. Such enzymatic activities include, but are not limited to, methyltransferase activity, demethylase activity, acetyltransferase activity, deacetylase activity, kinase activity, phosphatase activity, ubiquitin ligase activity, deubiquitinating activity, adenylation activity, deadenylation activity, SUMOylating activity, deSUMOylating activity, ribosylation activity, de-ribosylation activity, myristoylation activity, and demyristoylation activity. [0144] In some cases, the fusion partner has enzymatic activity that modifies a protein associated with a target nucleic acid. The protein may be a histone, an RNA binding protein, or a DNA binding protein. Examples of such protein modification activities include methyltransferase activity such as that provided by a histone methyltransferase (HMT) (e.g., suppressor of variegation 3-9 homolog 1 (SUV39H1, also known as KMT1A), euchromatic histone lysine methyltransferase 2 (G9A, also known as KMT1C and EHMT2), SUV39H2, ESET/SETDB1, SET1A, SET1B, MLL1 to 5, ASH1, SYMD2, NSD1, DOT1L, Pr-SET7/8, SUV4-20H1, EZH2, RIZ1); demethylase activity such as that provided by a histone demethylase (e.g., Lysine Demethylase 1A (KDM1A also known as LSD1), JHDM2a/b, JMJD2A/JHDM3A, JMJD2B, JMJD2C/GASC1, JMJD2D, JARID1A/RBP2, JARID1B/PLU-1, JARID1C/SMCX, JARID1D/SMCY, UTX, JMJD3); acetyltransferase activity such as that provided by a histone acetylase transferase (e.g., catalytic core/fragment of the human acetyltransferase p300, GCN5, PCAF, CBP, TAF1, TIP60/PLIP, MOZ/MYST3, MORF/MYST4, HBO1/MYST2, HMOF/MYST1, SRC1, ACTR, P160, CLOCK); deacetylase activity such as that provided by a histone deacetylase (e.g., HDAC1, HDAC2, HDAC3, HDAC8, HDAC4, HDAC5, HDAC7, HDAC9, SIRT1, SIRT2, HDAC11); kinase activity, phosphatase activity, ubiquitin ligase activity, deubiquitinating activity, adenylation activity, deadenylation activity, SUMOylating activity, deSUMOylating activity, ribosylation activity, deribosylation activity, myristoylation activity, and demyristoylation activity. [0145] In some cases, a terminus of the Type V CRISPR/Cas protein is linked to a terminus of the fusion partner through an amide bond. In some cases, a Type V CRISPR/Cas protein is coupled to a fusion partner via a linker protein. The linker protein may have any of a variety of amino acid sequences. A linker protein may comprise a region of rigidity (e.g., beta sheet, alpha helix), a region of flexibility, or any combination thereof. In some instances, the linker comprises small amino acids, such as glycine and alanine, that impart high degrees of flexibility. The ordinarily skilled artisan will recognize that design of a peptide conjugated to any desired element may include linkers that are all or partially flexible, such that the linker may include a flexible linker as well as one or more portions that confer less flexible structure. Suitable linkers include proteins of 4 linked amino acids to 40 linked amino acids in length, or between 4 linked amino acids and 25 linked amino acids in length. These linkers may be produced by using synthetic, linker-encoding oligonucleotides to couple the proteins, or may be encoded by a nucleic acid sequence encoding a fusion protein (e.g., an effector protein coupled to a fusion partner). Examples of linker proteins include glycine polymers (G)n, glycine-serine polymers (including, for example, (GS)n, GSGGSn, GGSGGSn, and GGGSn, where n is an integer of at least one), glycine-alanine polymers, and alanine-serine polymers. Exemplary linkers may comprise amino acid sequences including, but not limited to, GGSG, GGSGG, GSGSG, GSGGG, GGGSG, and GSSSG. Multimeric Complexes [0146] Compositions, systems, and methods of the present disclosure may comprise a multimeric complex or uses thereof, wherein the multimeric complex comprises multiple effector proteins that non-covalently interact with one another. A multimeric complex may comprise enhanced activity relative to the activity of any one of its effector proteins alone. For example, a multimeric complex comprising two Cas proteins may comprise greater nucleic acid binding affinity, cis-cleavage activity, and/or transcollateral cleavage activity than that of either of the Cas proteins provided in monomeric form. A multimeric complex may have an affinity for a target region of a target nucleic acid and is capable of catalytic activity (e.g., cleaving, nicking or modifying the nucleic acid) at or near the target region. Multimeric complexes may be activated when complexed with a guide nucleic acid. Multimeric complexes may be activated when complexed with a guide nucleic acid and a target nucleic acid. In some instances, the multimeric complex cleaves the target nucleic acid. In some instances, the multimeric complex nicks the target nucleic acid. [0147] Provided herein are compositions comprising a multimeric complex, wherein the multimeric complex comprises: a Cas12 protein comprising an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 92%, at least 95%, at least 97%, at least 98%, at least 99%, or 100% identical to any one of the sequences found in Table 1 and a Type V CRISPR/Cas protein of the present disclosure. [0148] A type V CRISPR/Cas protein, a dimer thereof, or a multimeric complex thereof may cleave both strands of a target DNA molecule at different locations (thereby generating a sticky ended product) or at the complementary positions (thereby generating a blunt end product). A type V CRISPR/Cas protein, a dimer thereof, or a multimeric complex thereof may cleave a double-stranded nucleic acid to generate product nucleic acids comprising 5’ overhangs. The 5’ overhangs may be 1-4 nucleotides, 1-6 nucleotides, 2-6 nucleotides, 3-8 nucleotides, or greater than 4 nucleotides in length. [0149] A type V CRISPR/Cas protein, a dimer thereof, or a multimeric complex thereof, may cleave each strand of a target DNA molecule with different kinetics. For example, an effector protein may cleave a first strand of a target DNA molecule with faster kinetics than the second strand. In such cases, the type V CRISPR/Cas protein, the dimer thereof, or the multimeric complex thereof releases the target nucleic acid subsequent to the first cleavage and prior to the second cleavage, thereby generating a “nicked” (e.g., cleaved only on one strand) product. [0150] The effector proteins provided herein (e.g., a type V CRISPR protein) enable the detection or modification of target nucleic acids (e.g., DNA or RNA). The detection or modification of the target nucleic acid is facilitated by an effector protein. [0151] An effector protein can comprise an effector protein capable of being activated when complexed with gRNA, and a target nucleic acid. [0152] The effector protein can become activated after binding of the gRNA systems disclosed herein to the target nucleic acid, in which the activated effector protein can exhibit sequence-dependent cleavage activity, also referred to herein as “cis cleavage activity” or “target cleavage activity.” Target cleavage activity can be specific cleavage of a target nucleic acid at or near the region of the target nucleic acid that hybridizes to the spacer of the gRNA system. Target cleavage may introduce a double stranded break into the target nucleic acid. In some embodiments, target cleavage may introduce a double stranded break with a 5’ overhang into the target nucleic acid. In some embodiments, the target nucleic acid may be modified at or near the double stranded break. [0153] The effector protein can become activated after binding of the gRNA systems disclosed herein target nucleic, in which the activated effector protein can exhibit sequence- independent cleavage activity, also referred to herein as “trans cleavage activity” or “collateral cleavage activity.” Trans cleavage activity can be non-specific cleavage of nearby single- stranded nucleic acids by the activated effector protein, such as trans cleavage of nucleic acids in a reporter nucleic acid, where the reporter nucleic acid also comprises a detection moiety. Once the nucleic acid of the reporter nucleic acid is cleaved by the activated effector protein, the detection moiety is released from the nucleic acid of the reporter nucleic acid, and generates a detectable signal. Often the detection moiety is at least one of a fluorophore, a dye, a polypeptide, or a nucleic acid. Sometimes the detection moiety binds to a capture molecule immobilized on a solid surface. The detectable signal can be visualized on the solid surface to assess the presence, the absence, or level of presence of the target nucleic acid. A detectable signal can be a calorimetric, potentiometric, amperometric, optical (e.g., fluorescent, colorimetric, etc.), or piezo-electric signal. Often, the detectable signal is present prior to cleavage of the nucleic acid of the reporter nucleic acid and changes upon cleavage of the nucleic acid of the reporter nucleic acid. Sometimes, the signal is absent prior to cleavage of the nucleic acid of the reporter nucleic acid and is present upon cleavage of the nucleic acid of the reporter nucleic acid. The detectable signal can be immobilized on a solid surface for detection. [0154] The effector proteins disclosed herein may elicit reporter nucleic acid activity upon cleavage of the nucleic acid of the reporter nucleic acid. Reporter nucleic acid activity refers to trans cleavage activity of the reporter nucleic acid. Reporter nucleic acid activity may be a calorimetric, potentiometric, amperometric, optical (e.g., fluorescent, colorimetric, etc.), or piezo-electric signal. For example, cleavage of the nucleic acid of the reporter nucleic acid by the effector protein may elicit a fluorescent signal. Reporter nucleic acid activity may increase or decrease over time in response to an effector protein trans cleavage activity. Reporter nucleic acid activity may accumulate over time in response to an effector protein trans cleavage activity. A maximal reporter nucleic acid activity may occur when a reporter nucleic acid signal (e.g., a calorimetric, potentiometric, amperometric, optical (e.g., fluorescent, colorimetric, etc.), or piezo-electric signal) is highest within a designated assay. In some embodiments, a maximal reporter nucleic acid signal may occur when a reporter nucleic acid signal reaches a maximum signal, after which the reporter nucleic acid signal decreases. In some embodiments, a maximal reporter nucleic acid signal may occur when a reporter nucleic acid signal increases to saturation after which the signal is no longer increasing. [0155] The effector protein can be a CRISPR/Cas (clustered regularly interspaced short palindromic repeats - CRISPR associated) ribonucleoprotein (RNP) complex with trans cleavage activity, which can be activated by binding of the spacer a gRNA to a target nucleic acid. The effector protein can be a CRISPR/Cas (clustered regularly interspaced short palindromic repeats - CRISPR associated) nucleoprotein complex with cis cleavage activity, which can be activated by binding of the spacer of a gRNA to a target nucleic acid. The CRISPR/Cas ribonucleoprotein (RNP) complex can comprise a Cas protein complexed with an engineered guide RNA (gRNA) comprising a gRNA and an intermediary nucleic acid. Sometimes, the gRNA and the intermediary nucleic acid are engineered as a single polyribonucleotide, referred to herein as a compositeegRNA. An assay using the CRISPR/Cas RNP complex to detect target nucleic acids can comprise gRNAs, intermediary RNAs, Cas proteins, and reporter nucleic acids. The CRISPR/Cas RNP complex used to modify target nucleic acids can comprise gRNAs, intermediary RNAs, Cas proteins, and target nucleic acids in a sample from a subject. [0156] The effector proteins described herein may be activated to exhibit cleavage activity (e.g., cis cleavage of a target nucleic acid or trans cleavage of a collateral nucleic acid) upon binding of an effector protein and gRNA to a target nucleic acid (e.g., DNA). Once activated, the effector protein may specifically cleave the reporter nucleic acid. The effector protein may have cleavage activity once activated [0157] In some cases, the effector protein is from at least one of Leptotrichia shahii (Lsh), Listeria seeligeri (Lse), Leptotrichia buccalis (Lbu), Leptotrichia wadeu (Lwa), Rhodobacter capsulatus (Rca), Herbinix hemicellulosilytica (Hhe), Paludibacter propionicigenes (Ppr), Lachnospiraceae bacterium (Lba), [Eubacterium] rectale (Ere), Listeria newyorkensis (Lny), Clostridium aminophilum (Cam), Prevotella sp. (Psm), Capnocytophaga canimorsus (Cca, Lachnospiraceae bacterium (Lba), Bergeyella zoohelcum (Bzo), Prevotella intermedia (Pin), Prevotella buccae (Pbu), Alistipes sp. (Asp), Riemerella anatipestifer (Ran), Prevotella aurantiaca (Pau), Prevotella saccharolytica (Psa), Prevotella intermedia (Pin2), Capnocytophaga canimorsus (Cca), Porphyromonas gulae (Pgu), Prevotella sp. (Psp), Porphyromonas gingivalis (Pig), Prevotella intermedia (Pin3), Enterococcus italicus (Ei), Lactobacillus salivarius (Ls), or Thermus thermophilus (Tt). Sometimes the effector protein is a CasY protein. [0158] In some embodiments, the effector proteins disclosed herein may be combined to detect the same or different target nucleic acids in the same reaction. [0159] The present disclosure provides compositions of RNA components that can be coupled with an effector protein or effector protein to support high levels of nuclease activity by an effector protein. These RNA components include gRNA and tracrRNA and form the guide RNA (gRNA) systems described herein. The RNA components of the present disclosure may comprise nucleotides. The term “nucleotide” may be used interchangeably with “nucleotide residue,” “nucleic acid,” “nucleic acid residue,” “base,” or “nucleotide base.” The gRNAs and tracrRNAs disclosed herein have been engineered for superior activity when used with Cas12 proteins and have been designed to be used as separate RNA components (referred to as a “gRNA system”) or as linked RNA components (referred to as a “gRNA”). Formation of a complex comprising an effector protein), a gRNA system or a gRNA, and a target nucleic acid may activate cis cleavage activity by the effector protein of the target nucleic acid. For the purposes of this disclosure, the disclosure provides the use of effector proteins and their RNA components for the detection of specific characteristics in a nucleic acid (i.e., polymorphisms). IV. Guide Nucleic Acids [0160] The compositions, and methods of the present disclosure may comprise a guide nucleic acid or a use thereof. In general, a guide nucleic acid is a nucleic acid molecule that binds to an effector protein (e.g., a CRISPR/Cas protein), thereby forming a ribonucleoprotein complex (RNP) a target nucleic acid, thereby targeting the RNP to the target nucleic acid. A guide RNA generally comprises a crispr RNA (crRNA), at least a portion of which is complementary to a target sequence of a target nucleic acid. In some instances, the guide RNA comprises a trans-activating crispr RNA (tracrRNA) that interacts with the effector protein. In some cases, the guide RNA is a single guide RNA (sgRNA) (e.g., a crRNA linked to a tracrRNA). In some instances, a crRNA and tracrRNA function as two separate, unlinked molecules. Guide nucleic acids are often referred to as “guide RNA” Or “gRNA.” However, a guide nucleic acid may comprise deoxyribonucleotides. The term “guide RNA,” as well as crRNA and tracrRNA, includes guide nucleic acids comprising DNA bases and RNA bases. [0161] In general, the crRNA comprises a spacer region that hybridizes to a target sequence of a target nucleic acid, and a repeat region that interacts with the effector protein. The repeat region may also be referred to as a “protein-binding segment.” Typically, the repeat region is adjacent to the spacer region. For example, a guide RNA that interacts with a Cas12a protein comprises a repeat region that is 5’ of the spacer region. [0162] In some instances, the tracrRNA comprises a stem-loop structure comprising a stem region and a loop region. In some cases, the stem region is 4 to 8 linked nucleosides in length. In some cases, the stem region is 5 to 6 linked nucleosides in length. In some cases, the stem region is 4 to 5 linked nucleosides in length. In some cases, the tracrRNA comprises a pseudoknot (e.g., a secondary structure comprising a stem at least partially hybridized to a second stem or half-stem secondary structure). An effector protein or a multimeric complex thereof may recognize a tracrRNA comprising multiple stem regions. In some instances, the amino acid sequences of the multiple stem regions are identical to one another. In some instances, the amino acid sequences of at least one of the multiple stem regions is not identical to those of the others. In some cases, the tracrRNA comprises at least 2, at least 3, at least 4, or at least 5 stem regions. [0163] An effector protein may form a multimeric complex that binds a guide RNA. The effector protein s of the multimeric complex may bind the guide RNA in an asymmetric fashion. In some cases, one effector protein of the multimeric complex interacts more strongly with the guide RNA than another effector protein of the multimeric complex. In some cases, an effector protein or a multimeric complex thereof interacts more strongly with a target nucleic acid when it is complexed with the guide RNA relative to when the effector protein or the multimeric complex is not complexed with the guide RNA. [0164] In some cases, an effector protein or a multimeric complex thereof recognizes a PAM on a target nucleic acid. In some cases, multiple effector proteins of the multimeric complex recognize a PAM on a target nucleic acid. In some cases, only one programmable nuclease of the multimeric complex recognizes a PAM on a target nucleic acid. In some cases, the PAM is 3’ to the spacer region of the crRNA. In some cases, the PAM is directly 3’ to the spacer region of the crRNA. [0165] The spacer region of the guide RNA may comprise complementarity with (e.g., hybridize to) a target sequence of a target nucleic acid. In some cases, the spacer region is 15-28 linked nucleosides in length. In some cases, the spacer region is 15-26, 15-24, 15-22, 15-20, 15- 18, 16-28, 16-26, 16-24, 16-22, 16-20, 16-18, 17-26, 17-24, 17-22, 17-20, 17-18, 18-26, 18-24, or 18-22 linked nucleosides in length. In some cases, the spacer region is 18-24 linked nucleosides in length. In some cases, the spacer region is at least 15 linked nucleosides in length. In some cases, the spacer region is at least 16, 18, 20, or 22 linked nucleosides in length. In some cases, the spacer region comprises at least 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some cases, the spacer region is at least 17 linked nucleosides in length. In some cases, the spacer region is at least 18 linked nucleosides in length. In some cases, the spacer region is at least 20 linked nucleosides in length. In some cases, the spacer region is at least 80%, at least 85%, at least 90%, at least 95% or 100% complementary to a target sequence of the target nucleic acid. In some cases, the spacer region is 100% complementary to the target sequence of the target nucleic acid. In some cases, the spacer region comprises at least 15 contiguous nucleotides that are complementary to the target nucleic acid. [0166] The guide RNA may be an engineered guide nucleic acid (e.g., chemically or recombinantly produced). The sequence of the engineered guide nucleic acid, or a portion thereof, may be different from the sequence of a naturally occurring nucleic acid. The engineered guide nucleic acid may bind to a Type V CRISPR/Cas protein disclosed herein. [0167] The guide RNA may bind to a target nucleic acid (e.g., a single strand of a target nucleic acid) or a portion thereof. The target nucleic acid may comprise a mutation, such as a single nucleotide polymorphism (SNP). A mutation may confer for example, resistance to a treatment, such as antibiotic treatment. The guide nucleic acid may bind to a target nucleic acid, such as DNA or RNA, from a cancer gene or gene associated with a genetic disorder, or an amplicon thereof, as described herein. [0168] In some instances, the guide RNA does not comprise a tracrRNA. In some cases, an effector protein does not require a tracrRNA to locate and/or cleave a target nucleic acid. In some instances, the crRNA of the guide nucleic acid comprises a repeat region and a spacer region, wherein the repeat region binds to the effector protein and the spacer region hybridizes to a target sequence of the target nucleic acid. The repeat sequence of the crRNA may interact with an effector protein, allowing for the guide nucleic acid and the effector protein to form an RNP complex. [0169] In some cases, an effector protein or a multimeric complex thereof cleaves a precursor RNA (“pre-crRNA”) to produce a guide RNA, also referred to as a “mature guide RNA.” An effector protein that cleaves pre-crRNA to produce a mature guide RNA is said to have pre-crRNA processing activity. In some cases, a repeat region of a guide RNA comprises mutations or truncations relative to respective regions in a corresponding pre-crRNA. [0170] The guide nucleic acid may comprise a first region complementary to a target nucleic acid (FR1) and a second region that is not complementary to the target nucleic acid (FR2). In some cases, FR1 is located 5’ to FR2 (FR1-FR2). In some cases, FR2 is located 5’ to FR1 (FR2-FR1). [0171] In some cases, the guide comprises 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 linked nucleosides. In general, a guide nucleic acid comprises at least linked nucleosides. In some instances, a guide nucleic acid comprises at least 25 linked nucleosides. A guide nucleic acid may comprise 10 to 50 linked nucleosides. In some cases, the guide nucleic acid comprises or consists essentially of about 12 to about 80 linked nucleosides, about 12 to about 50, about 12 to about 45, about 12 to about 40, about 12 to about 35, about 12 to about 30, about 12 to about 25, from about 12 to about 20, about 12 to about 19 , about 19 to about 20, about 19 to about 25, about 19 to about 30, about 19 to about 35, about 19 to about 40, about 19 to about 45, about 19 to about 50, about 19 to about 60, about 20 to about 25, about 20 to about 30, about 20 to about 35, about 20 to about 40, about 20 to about 45, about 20 to about 50, or about 20 to about 60 linked nucleosides. In some cases, the guide nucleic acids about 10 to about 60, about 20 to about 50, or about 30 to about 40 linked nucleosides. [0172] It is understood that the sequence of a spacer region need not be 100% complementary to that of a target sequence of a target nucleic acid to hybridize or hybridize specifically to the target sequence. The guide nucleic acid may comprise at least one uracil between nucleic acid residues 5 to 20 of the spacer region that is not complementary to the corresponding nucleoside of the target sequence. The guide nucleic acid may comprise at least one uracil between nucleic acid residues 5 to 9, 10 to 14, or 15 to 20 of the spacer region that is not complementary to the corresponding nucleoside of the target sequence. In some cases, the region of the target nucleic acid that is complementary to the spacer region comprises an epigenetic modification or a post-transcriptional modification. In some cases, the epigenetic modification comprises an acetylation, methylation, or thiol modification. Table 4: Exemplary Guide Nucleic Acid/ Effector Protein Combinations

[0173] Provided herein, are gRNAs that have been engineered to guide effector proteins to a target nucleic acid sequence. Provided herein, are gRNAs that have been engineered to distinguish the at-risk allele from the non-risk allele and the wild type sequence using a DETECTR assay. Provided herein, detection of PNPLA3 alleles using gRNAs to detect the presence or absence of the at-risk allele (rs738409) while ignoring the non-risk allele (rs738408). In some embodiments, the wild type (“WT”) gRNA detects WT or non-risk alleles lacking the at-risk allele, and the mutant gRNA detects the at-risk allele with or without the non-risk allele. [0174] In some embodiments, guide RNAs compatible with a Cas12 effector protein were designed to detect the PNPLA3 SNPs. In some embodiments, guide RNAs compatible with a CasY effector protein were designed to detect the PNPLA3 SNPs. In some embodiments, guide RNAs to detect the PNPLA3 SNPs were compatible with a Cas 12 effector protein and a CasY effector protein. In some embodiments, gRNAs to detect the PNPLA3 SNPs were compatible with multiple effector proteins. In some embodiments, gRNAs to detect the target nucleic acid comprising nucleotide variant were compatible with multiple effector proteins. In some embodiments, gRNAs were paired with a specific effector protein to increase assay efficiency. In some embodiments, gRNAs were paired with a specific effector protein to increase affinity. [0175] In some embodiments, multiple gRNAs, each specific for a single sequence alteration, are pooled for detection of target nucleic acid. In some embodiments, multiple gRNAs are pooled to distinguish two sequence alterations in target nucleic acid. In some embodiments, multiple gRNAs are pooled to distinguish mutations in target nucleic acid. In some embodiments, multiple gRNAs are pooled to distinguish SNPs in target nucleic acid. In some embodiments, multiple gRNAs are pooled to distinguish sequence alterations in PNPLA3. In some embodiments, multiple gRNAs are pooled to distinguish mutations in PNPLA3. In some embodiments, multiple gRNAs are pooled to distinguish SNPs in PNPLA3. In some embodiments, multiple gRNAs are pooled to distinguish two SNPs in PNPLA3. In some embodiments, multiple gRNAs, each specific for a single PNPLA3 allele, are pooled for detection of at-risk alleles. In some embodiments, multiple gRNAs, each specific for a single PNPLA3 allele, are pooled for detection of non-risk alleles. In some embodiments, multiple gRNAs, each specific for a single PNPLA3 allele, are pooled for detection of wild-type alleles. In some embodiments, multiple gRNAs, each specific for a single PNPLA3 allele, are pooled for detection of wild-type alleles and non-risk alleles. In some embodiments, multiple gRNAs, each specific for a single PNPLA3 allele, are pooled for detection of wild-type alleles, at-risk allele and non-risk alleles. In some embodiments, gRNAs for detection of PNPLA3 wild-type alleles and non-risk alleles are gRNAs directed to wild-type alleles and rs738408 allele. In some embodiments, gRNAs for detection of PNPLA3 wild-type alleles and non-risk alleles, are pooled for detection of wild-type alleles and non-risk alleles in the absence of the at-risk allele. In some embodiments, gRNAs directed to the rs738409 allele and the rs738409+408 allele are pooled for the detection of the at-risk allele independent of the presence or absence of the non-risk allele. In some embodiments, gRNAs pools are designed to detect the wild type or non-risk alleles or at- risk allele independent of the presence or absence of the non-risk allele. [0176] In some embodiments, multiple gRNAs, each specific for a single target allele, are pooled for detection of wild-type alleles, non-risk alleles, and at-risk alleles in homozygous or heterozygous samples. In some embodiments, multiple gRNAs, each specific for a single target allele, are pooled for detection and identification of samples containing different combinations of at-risk, non-risk, and wild type alleles, wherein fluorescence data was used to genotype the samples as homozygous or heterozygous. In some embodiments, multiple gRNAs, each specific for a single PNPLA3 allele, are pooled for detection of wild-type alleles, non-risk alleles, and at-risk alleles in homozygous or heterozygous samples. In some embodiments, multiple gRNAs, each specific for a single PNPLA3 allele, are pooled for detection of nine different homozygous and heterozygous genotypes with respect to PNPLA3. In some embodiments, multiple gRNAs, each specific for a single PNPLA3 allele, are pooled for detection of the wild type or non-risk alleles (“WT PNPLA3”) or at-risk allele (“I148M PNPLA3”) independent of the presence or absence of the non-risk allele. In some embodiments, multiple gRNAs, each specific for a single PNPLA3 allele, are pooled for detection of the wild type or non-risk alleles in the presence of the at-risk allele. In some embodiments, multiple gRNAs, each specific for a single PNPLA3 allele, are pooled for detection and identification of homozygous and heterozygous samples containing different combinations of at-risk, non-risk, and wild type alleles. In some embodiments, multiple gRNAs, each specific for a single PNPLA3 allele, are pooled for detection and identification of samples containing different combinations of at-risk, non-risk, and wild type alleles, wherein fluorescence data was used to genotype the samples as homozygous or heterozygous for the PNPLA3 SNPs. Using fluorescence signal data, samples were characterized as being wild type, homozygous, or heterozygous for the at-risk allele (rs738409). [0177] Provided herein are gRNAs that have been engineered to guide effector proteins to a target nucleic acid sequence. A gRNA can comprise a spacer. The spacer can have a sequence that hybridizes to a sequence of a target nucleic acid. The sequence of the target nucleic acid that hybridizes to the spacer may also be referred to as the target region. The spacer can have a sequence that is reverse complementary, or sufficiently reverse complementary to allow for hybridization, to a sequence of a target nucleic acid. In some embodiments, a portion of the spacer sequence hybridizes to a sequence of a target nucleic acid. The portion of the spacer sequence can have a sequence that is reverse complementary, or sufficiently reverse complementary to allow for hybridization, to the sequence of the target nucleic acid. Spacers [0178] A gRNA may comprise a spacer sequence. The spacer may hybridize to a sequence of a target nucleic acid. Although 100% reverse complementarity is not needed for hybridization, a spacer can have a sequence that is at least 70% reverse complementary to a region of a target nucleic acid sequence to which the spacer hybridizes. A spacer can have a sequence that is at least 75% reverse complementary, at least 80% reverse complementary, at least 85% reverse complementary, at least 90% reverse complementary, at least 92% reverse complementary, at least 95% reverse complementary, at least 97% reverse complementary, at least 99% reverse complementary, at least 100% reverse complementary, from 70% to 100% reverse complementary, from 80% to 90% reverse complementary, from 85% to 95% reverse complementary, from 75% to 99% reverse complementary, from 90% to 99% reverse complementary, from 90% to 100% reverse complementary, or from 85% to 100% reverse complementary to a region of a target nucleic acid sequence to which the spacer hybridizes. [0179] The spacer can have a length of from 5 to 100 nucleotides. In some embodiments, the spacer has a length of from 5 to 50 nucleotides. In some embodiments, the spacer has a length of from 5 to 25 nucleotides. In some embodiments, the spacer has a length of from 25 to 100 nucleotides. In some embodiments, the spacer has a length of from 50 to 100 nucleotides. In some embodiments, the spacer has a length of from 75 to 100 nucleotides. In a preferred embodiment, the spacer has a length of from 16 to 20 nucleotides. In some embodiments, the spacer has a length of at least 5, at least 10, at least 15, at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 55, at least 60, at least 65, at least 70, or at least 75 nucleotides. In a preferred embodiment, the spacer has a length of at least 16 nucleotides. In some embodiments, the spacer has a length of about 16 nucleotides, about 17 nucleotides, about 18 nucleotides, about 19 nucleotides, or about 20 nucleotides. In a first preferred embodiment, the spacer has a length of 17 nucleotides. In a second preferred embodiment, the spacer has a length of 18 nucleotides. In a third preferred embodiment, the spacer has a length of 19 nucleotides. [0180] The spacer may be part of a discrete gRNA system. The gRNA forms a complex with the target nucleic acid and a second effector protein or ortholog thereof, thereby activating the second effector protein or ortholog thereof. In some embodiments, the gRNA may form a complex with the target nucleic acid and a third effector protein or ortholog thereof, thereby activating the third effector protein or ortholog thereof. The two or more effector proteins or orthologs thereof may comprise different functions. In some embodiments, the two or more effector proteins may comprise fusion proteins. For example, a first programmable effector protein may comprise a first effector protein fused to a first fusion protein, and a second effector protein may comprise a second effector protein fused to a second fusion protein. A fusion protein may comprise an activity (e.g., an enzymatic activity) for use in a biochemical assay, such as for research purposes. For example, a fusion protein may be a reporter protein used to visualize the location of a target nucleic acid site. In some embodiments, an effector protein ortholog comprising a reporter protein fusion protein may use used to label or modify multiple target nucleic acids simultaneously. A fusion protein may comprise an activity (e.g., an enzymatic activity) for use in a genome modification strategy. For example, the fusion protein may comprise a base editing activity, transcriptional modulation activity, or any activity to be specifically targeted to a target site. In some embodiments, the first effector protein ortholog may perform a first activity upon activation, and the second effector protein ortholog may perform a second activity upon activation. For example, the first effector protein ortholog may exhibit target cleavage activity upon activation, and the second effector protein may exhibit trans cleavage activity upon activation, thereby enabling simultaneous modification and detection of a target nucleic acid using two effector protein orthologs and a gRNA. [0181] In some embodiments, an effector protein ortholog may be an enzymatically dead nuclease (e.g., an effector protein lacking cis cleavage activity and/or trans cleavage activity). An enzymatically dead effector protein may be capable of binding to a target nucleic acid sequence when complexed with an gRNA but that does not catalyze a cis cleavage reaction or a trans cleavage reaction upon binding to the target nucleic acid sequence. In some embodiments, an enzymatically dead effector protein may comprise a point mutation in an endonuclease domain of the effector protein. In some embodiments the enzymatically dead effector protein may be fused to a fusion protein having additional enzymatic activity. The protein having additional activity may catalyze a reaction upon recruitment to the target nucleic acid by the enzymatically dead effector protein. The enzymatically dead effector protein may be a dead Cas12 protein.). [0182] In some embodiments, an ortholog-specific repeat may comprise nucleotides that form sequence-specific interactions with a single effector protein ortholog, a subset of effector protein orthologs or gRNAs complexed with an effector protein. A gRNA comprising the ortholog-specific repeat sequence may activate an effector protein ortholog when complexed with the effector protein and a target nucleic acid. For example, a gRNA may activate a Type V Cas system. A gRNA may direct two or effector protein orthologs to the same region of a target nucleic acid. In some embodiments, the two or more effector protein orthologs may be used for detection. The first effector protein ortholog and the second effector protein ortholog may have different activities. For example, the first effector protein ortholog may exhibit trans cleavage activity upon activation, and the second effector protein ortholog may exhibit target cleavage activity upon activation. In some embodiments, the first effector protein ortholog may be a first Cas12 protein ortholog. [0183] In some embodiments, an effector protein ortholog may be an enzymatically dead effector protein (e.g., an effector protein lacking endonuclease activity). An enzymatically dead effector protein may be capable of binding to a target nucleic acid sequence when complexed with an gRNA but that does not catalyze a cis cleavage reaction or a trans cleavage reaction upon binding to the target nucleic acid sequence. In some embodiments, an enzymatically dead effector protein may comprise a point mutation in an endonuclease domain of the effector protein. In some embodiments the enzymatically dead effector protein may be fused to a fusion protein having additional enzymatic activity. The protein having additional activity may catalyze a reaction upon recruitment to the target nucleic acid by the enzymatically dead effector protein. The enzymatically dead effector protein may be a dead Cas12 protein. [0184] In some instances of the method disclosed herein, a plurality of gRNA sequences are provided as a guide RNA pool. In some instances, the guide RNA pool comprises at least 1, at least 2, at least 3, at least 4, at least 5, at least 10, at least 25, at least 50, at least 100, at least 150, or at least 200 guide RNAs. In some embodiments, the guide RNA pool comprises 1, up to 2, up to 3, up to 4, up to 5, up to 10, up to 25, up to 50, up to 100, up to 150, up to 200 guide RNAs, or up to 250 guide RNAs. [0185] In some instances of the disclosure, the method disclosed herein can comprises a plurality guide RNAs can be specific for a wild-type nucleic gene sequence, or is specific for a gene sequence that comprises at least one SNP or mutation. In some embodiments, the plurality of gRNAs can target multiple genes and the different variants of said gene. In some embodiments, the plurality of different gRNAs that are specific for more than 1, more than 2, more than 3, more than 4, more than 5, more than 10, more than 20, more than 25 different targets (i.e., genes, nucleotide variants, etc.) [0186] An effector protein of the present disclosure may interact with (binds to) a corresponding gRNA to form a ribonucleoprotein (RNP) complex that is targeted to a particular region of target nucleic acid via base pairing between the spacer of the gRNA and a target sequence within the target nucleic acid molecule. For example, an RNP complex may comprise an effector protein and a gRNA. A gRNA may comprise a nucleotide sequence (a spacer sequence) that is complementary to a region of sequence of a target nucleic acid. Thus, an effector protein may form a complex with a gRNA, and the gRNA may provide sequence specificity to the RNP complex via the spacer sequence. The effector protein of the complex may provide the site-specific activity upon interaction with the corresponding target nucleic acid. In other words, the effector protein may be guided to a target site (e.g., stabilized at a target site) within a target nucleic acid sequence by virtue of its association with the gRNA. [0187] The effector protein may be activated upon binding of the RNP complex comprising the effector protein and the gRNA to the particular region of the target nucleic acid. In some embodiments, the target nucleic acid may be a chromosomal target a gene, a plasmid, or an untranslated region. Binding of the RNP complex to the region of the target nucleic acid may activate cis cleavage activity of the effector protein. Binding of the RNP complex to the region of the target nucleic acid may activate trans cleavage activity of the effector protein. V. Target Nucleic Acids [0188] The compositions, and methods of the present disclosure may comprise a target nucleic acid or a use thereof. In general, a target nucleic acid is a nucleic acid molecule that hybridizes to the guide nucleic acid sequence associated to the effector protein. [0189] In some embodiments, the target nucleic acid can be from 0.05% to 20% of total nucleic acids in the sample. Sometimes, the target nucleic acid is from 0.1% to 10% of the total nucleic acids in the sample. The target nucleic acid, in some cases, is from 0.1% to 5% of the total nucleic acids in the sample. [0190] A number of different target nucleic acids can be detected with the compositions and methods disclosed herein. In some embodiments, the target nucleic acid may be DNA. In some embodiments, the target nucleic acid may be RNA. The target nucleic acid may hybridize with a guide nucleic acid to direct an effector protein or effector protein, thereby contacting the effector protein to the target nucleic acid sequence. A nucleotide variant of a gene can comprise a mutation that alters the nucleotide sequence of the gene. [0191] In some embodiments, target nucleic acids can detect a target nucleic acid sequence within a gene, or any variant thereof. In some embodiments, the variant gene comprises at least 1, at least 2, at least 3, at least 4, at least 5, at least 6 mutations as compared to a reference sequence of a gene. [0192] In some embodiments, the mutation is a synonymous mutation or silent mutation. [0193] In some embodiments, the mutation is a non-synonymous mutation. The non- synonymous mutation can result in an amino acid substitution in the protein product of the gene. In some embodiments, the mutation is a missense mutation, a nonsense mutation, or a non-stop mutation. In some embodiments, the target nucleic acid comprises a non-synonymous mutation, synonymous mutation, missense mutation, nonsense mutation, non-stop mutation, or any combination thereof. [0194] In some embodiments, the mutation is implicated in the presence or risk thereof in an individual who has the presence of the mutation. In some embodiments, the mutation is a known single polynucleotide polymorphisms suspected to cause disease. In some embodiments, the gene that comprises a SNP encodes for a gene selected from the group consisting of EDN1 endothelin 1, NOS1 neuronal nitric oxide synthetase 1, KCN1 potassium channel protein, TAF1 thrombin-activatable fibrinolysis inhibitor, MBL mannose binding protein, HRT 3A, Cyclin D1, UGT1A1 UDP glucoronosyl transferase, MIF macrophage migration inhibitory factor, SNCA alpha-synuclein, LRRK2 leucine-rich repeat kinase 2, MMP1 matrix metalloproteinase 1, PAI plasminogen activator inhibitor, PAI1, Npps nucleotide pyrophosphatase, CDH Cad cadherin, CDH1 E-Cad, POAG primary open angle glaucoma, TNF tumor necrosis factor, TNF-α, MDR1 p-glycoprotein (multiple-drug-resistant), TSP thrombospondin, PCS prostacyclin synthase, IR immune response, INSR insulin receptor, CNP cyclic nucleotide phosphodiesterase, LPL lipase, MCR melanocortin, MC1R, TMEM transmembrane protein , C9ORF72 chromosome 9 open reading frame 72, MAPT Tau protein-related gene, GRN progranulin-related gene GRN, COL Collagen, p53, MYOC myocilin, FBN1 fibrillin1, STX1A syntaxin1A, CCN cyclin, CCND1 cyclin D1, a fragment thereof, or any combination thereof. [0195] The guide RNA may bind to a target nucleic acid (e.g., a single strand of a target nucleic acid) or a portion thereof. The target nucleic acid may comprise a mutation, such as a single nucleotide polymorphism (SNP). A mutation may cause a disease in an individuals. The guide nucleic acid may bind to a target nucleic acid, such as DNA or RNA, from a cancer gene or gene associated with a genetic disorder, or an amplicon thereof, as described herein. In some embodiments, the target nucleic acid molecule comprises a nucleotide variant at a position of interest. In some embodiments, the target nucleic acid molecule comprises at least one nucleotide variant at a position of interest. In some embodiments, the target nucleic acid molecule is comprised in a raw sample, or fragment thereof. In some embodiments, the target nucleic acid molecule is comprised in a purified or non-purified genomic sample, or fragment thereof. In some embodiments, the target nucleic acid molecule is comprised in a sample processed via amplification assay, resulting is the amplification of copies of target nucleic acid molecules per sample. [0196] In some embodiments, the target nucleic acid encodes a wild-type allele of a gene. In some embodiments, the target nucleic acid encodes a recessive allele of a gene. In some embodiments, the target nucleic acid encodes a dominant allele. [0197] In some instances, samples are used for diagnosing a disease by detection of a target nucleic acid. In some instances, the disease is cancer. The sample used for cancer testing may comprise at least one target nucleic acid that may bind to a guide nucleic acid of the reagents described herein. The target nucleic acid, in some cases, comprises a portion of a gene comprising a mutation associated with cancer, a gene whose overexpression is associated with cancer, a tumor suppressor gene, an oncogene, a checkpoint inhibitor gene, a gene associated with cellular growth, a gene associated with cellular metabolism, or a gene associated with cell cycle. Sometimes, the target nucleic acid encodes a cancer biomarker, such as a prostate cancer biomarker or non-small cell lung cancer. In some cases, the assay may be used to detect “hotspots” in target nucleic acids that may be predictive of lung cancer. In some cases, the target nucleic acid comprises a portion of a nucleic acid that is associated with a blood fever. In some cases, the target nucleic acid is a portion of a nucleic acid from a genomic locus, any DNA amplicon of, an RNA, an in vitro transcribed RNA, a reverse transcribed mRNA, or a cDNA from a locus of at least one of: ALK, APC, ATM, AXIN2, BAP1, BARD1, BLM, BMPR1A, BRCA1, BRCA2, BRIP1, CASR, CDC73, CDH1, CDK4, CDKN1B, CDKN1C, CDKN2A, CEBPA, CHEK2, CTNNA1, DICER1, DIS3L2, EGFR, EPCAM, FH, FLCN, GATA2, GPC3, GREM1, HOXB13, HRAS, system, MAX, MEN1, MET, MITF, MLH1, MSH2, MSH3, MSH6, MUTYH, NBN, NF1, NF2, NTHL1, PALB2, PDGFRA, PHOX2B, PMS2, POLD1, POLE, POT1, PRKAR1A, PTCH1, PTEN, PNPLA3, RAD50, RAD51C, RAD51D, RB1, RECQL4, RET, RUNX1, SDHA, SDHAF2, SDHB, SDHC, SDHD, SMAD4, SMARCA4, SMARCB1, SMARCE1, STK11, SUFU, TERC, TERT, TMEM127, TP53, TSC1, TSC2, VHL, WRN, and WT1. [0198] In some instances, samples are used to diagnose a genetic disorder, also referred to as genetic disorder testing. The sample used for genetic disorder testing may comprise at least one target nucleic acid that may bind to a guide nucleic acid of the reagents described herein. In some embodiments, the genetic disorder is hemophilia, sickle cell anemia, β-thalassemia, Duchene muscular dystrophy, severe combined immunodeficiency, Huntington’s disease, or cystic fibrosis. The target nucleic acid, in some cases, is from a gene with a mutation associated with a genetic disorder, from a gene whose overexpression is associated with a genetic disorder, from a gene associated with abnormal cellular growth resulting in a genetic disorder, or from a gene associated with abnormal cellular metabolism resulting in a genetic disorder. In some cases, the target nucleic acid is a nucleic acid from a genomic locus, a transcribed mRNA, an in vitro transcribed RNA, or a reverse transcribed mRNA, or a DNA amplicon of or a cDNA from a locus of at least one of: CFTR, FMR1, SMN1, ABCB11, ABCC8, ABCD1, ACAD9, ACADM, ACADVL, ACAT1, ACOX1, ACSF3, ADA, ADAMTS2, ADGRG1, AGA, AGL, AGPS, AGXT, AIRE, ALDH3A2, ALDOB, ALG6, ALMS1, ALPL, AMT, AQP2, ARG1, ARSA, ARSB, ASL, ASNS, ASPA, ASS1, ATM, ATP6V1B1, ATP7A, ATP7B, ATRX, BBS1, BBS10, BBS12, BBS2, BCKDHA, BCKDHB, BCS1L, BLM, BSND, CAPN3, CBS, CDH23, CEP290, CERKL, CHM, CHRNE, CIITA, CLN3, CLN5, CLN6, CLN8, CLRN1, CNGB3, COL27A1, COL4A3, COL4A4, COL4A5, COL7A1, CPS1, CPT1A, CPT2, CRB1, CTNS, CTSK, CYBA, CYBB, CYP11B1, CYP11B2, CYP17A1, CYP19A1, CYP27A1, DBT, DCLRE1C, DHCR7, DHDDS, DLD, DMD, DNAH5, DNAI1, DNAI2, DYSF, EDA, EIF2B5, EMD, ERCC6, ERCC8, ESCO2, ETFA, ETFDH, ETHE1, EVC, EVC2, EYS, F9, FAH, FAM161A, FANCA, FANCC, FANCG, FH, FKRP, FKTN, G6PC, GAA, GALC, GALK1, GALT, GAMT, GBA, GBE1, GCDH, GFM1, GJB1, GJB2, GLA, GLB1, GLDC, GLE1, GNE, GNPTAB, GNPTG, GNS, GRHPR, HADHA, HAX1, HBA1,, HBA2, HBB, HEXA, HEXB, HGSNAT, HLCS, HMGCL, HOGA1, HPS1, HPS3, HSD17B4, HSD3B2, HYAL1, HYLS1, IDS, IDUA, IKBKAP, IL2RG, IVD, KCNJ11, LAMA2, LAMA3, LAMB3, LAMC2, LCA5, LDLR, LDLRAP1, LHX3, LIFR, LIPA, LOXHD1, LPL, LRPPRC, MAN2B1, MCOLN1, MED17, MESP2, MFSD8, MKS1, MLC1, MMAA, MMAB, MMACHC, MMADHC, MPI, MPL, MPV17, MTHFR, MTM1, MTRR, MTTP, MUT, MYO7A, NAGLU, NAGS, NBN, NDRG1, NDUFAF5, NDUFS6, NEB, NPC1, NPC2, NPHS1, NPHS2, NR2E3, NTRK1, OAT, OPA3, OTC, PAH, PC, PCCA, PCCB, PCDH15, PDHA1, PDHB, PEX1, PEX10, PEX12, PEX2, PEX6, PEX7, PFKM, PHGDH, PKHD1, PMM2, PNPLA3, POMGNT1, PPT1, PROP1, PRPS1, PSAP, PTS, PUS1, PYGM, RAB23, RAG2, RAPSN, RARS2, RDH12, RMRP, RPE65, RPGRIP1L, RS1, RTEL1, SACS, SAMHD1, SEPSECS, SGCA, SGCB, SGCG, SGSH, SLC12A3, SLC12A6, SLC17A5, SLC22A5, SLC25A13, SLC25A15, SLC26A2, SLC26A4, SLC35A3, SLC37A4, SLC39A4, SLC4A11, SLC6A8, SLC7A7, SMARCAL1, SMPD1, STAR, SUMF1, TAT, TCIRG1, TECPR2, TFR2, TGM1, TH, TMEM216, TPP1, TRMU, TSFM, TTPA, TYMP, USH1C, USH2A, VPS13A, VPS13B, VPS45, VRK1, VSX2, WNT10A, XPA, XPC, and ZFYVE26. In some embodiments, the target nucleic acid is, or is encoded by, a PNPLA3 (patatin-like phospholipase domain-containing protein 3) gene or a fragment thereof. In some embodiments, the target nucleic acid is a fragment of a PNPLA3 gene. In some embodiments, the PNPLA3 gene comprises a substitution of a C with a G at nucleotide position 444 of a wild-type PNPLA3 gene. In some embodiments, the PNPLA3 gene encodes a PNPLA3 protein comprising an I to M substitution at amino acid position of 148 of a wild-type PNPLA3 protein. In some embodiments, the PNPLA3 gene, or a fragment thereof, is a protein coding gene. In some embodiments, the PNPLA3 gene, or a fragment thereof, may include a silent mutation. In some embodiments, the PNPLA3 gene, or a fragment thereof, may include a SNP. In some embodiments, the PNPLA3 gene, or a fragment thereof, may include a non-synonymous mutation, synonymous mutation, missense mutation, nonsense mutation, non-stop mutation, or any combination thereof. [0199] In some embodiments, the target nucleic acid comprises the PNPLA3 gene comprising two different SNPs. In some embodiments, the target nucleic acid comprises the PNPLA3 gene comprising two SNP sites separated by only two nucleotide bases. In some embodiments, the target nucleic acid comprises the PNPLA3 gene comprising a first single nucleotide mutation (rs738409) leads to a I148M amino acid substitution associated with an increased risk of nonalcoholic fatty liver disease. In some embodiments, the target nucleic acid comprises the PNPLA3 gene comprising a second single nucleotide mutation (rs738408) codes a silent mutation with a 70% linkage to the at-risk allele. In some embodiments, the target nucleic acid comprises the PNPLA3 gene comprising different combinations of wild type (“WT”), at- risk mutant (rs738409), and non-risk mutant (rs738408) alleles. In some embodiments, the target nucleic acid comprises the PNPLA3 gene, wherein there are nine possible genetic combinations of wild type, at-risk mutant (rs738409), and non-risk mutant (rs738408) alleles. [0200] In some embodiments, the target nucleic acid is present in the cleavage reaction at a concentration of about 10 nM, about 20 nM, about 30 nM, about 40 nM, about 50 nM, about 60 nM, about 70 nM, about 80 nM, about 90 nM, about 100 nM, about 200 nM, about 300 nM, about 400 nM, about 500 nM, about 600 nM, about 700 nM, about 800 nM, about 900 nM, about 1 µM, about 10 µM, or about 100 µM. In some embodiments, the target nucleic acid is present in the cleavage reaction at a concentration of from 10 nM to 20 nM, from 20 nM to 30 nM, from 30 nM to 40 nM, from 40 nM to 50 nM, from 50 nM to 60 nM, from 60 nM to 70 nM, from 70 nM to 80 nM, from 80 nM to 90 nM, from 90 nM to 100 nM, from 100 nM to 200 nM, from 200 nM to 300 nM, from 300 nM to 400 nM, from 400 nM to 500 nM, from 500 nM to 600 nM, from 600 nM to 700 nM, from 700 nM to 800 nM, from 800 nM to 900 nM, from 900 nM to 1 µM, from 1 µM to 10 µM, from 10 µM to 100 µM, from 10 nM to 100 nM, from 10 nM to 1 µM, from 10 nM to 10 µM, from 10 nM to 100 µM, from 100 nM to 1 µM, from 100 nM to 10 µM, from 100 nM to 100 µM, or from 1 µM to 100 µM. In some embodiments, the target nucleic acid is present in the cleavage reaction at a concentration of from 20 nM to 50 µM, from 50 nM to 20 µM, or from 200 nM to 5 µM. VI. Certain Samples [0201] Also disclosed herein are methods of assaying for the presence or absence of the target nucleic acid comprising the nucleotide variant. In some embodiments, compositions comprising effector proteins, improved effector proteins, Cas effector proteins, improved Cas12, and any combination thereof, are used in methods of assaying for the presence or absence of a target nucleic acid in a sample. In some embodiments, the methods claimed herein detect target nucleic acid comprised in a sample. In some embodiments, the detection assay comprises direct or indirect detection. In some embodiments, direct detection comprises detection of the target nucleic acid within a crude or unprocessed clinical sample. In some embodiments, a crude or unprocessed sample is a non-purified sample. In some embodiments a crude or unprocessed sample comprises a sample directly collected from an organism. In some embodiments, the crude or unprocessed sample is collected from a buccal swab. In some embodiments, the crude or unprocessed sample is saliva directly collected from the organism. In some embodiments, the saliva directly collected from the organism comprises the DNA or RNA target nucleic acid for detection assay. [0202] In some embodiments, the detection assay comprises sample processing prior to detection. In some embodiments, sample processing prior to detection comprises purifying the sample collected from the organism. In some embodiments, the crude, unprocessed, or non- purified sample can be purified or processed. In some embodiments, the non-purified sample is purified prior to pre-amplification or pre-amplification method. In some embodiments, the detection assay comprises pre-amplification as disclosed herein. [0203] In some embodiments, detection comprises assaying for the presence or absence of the target nucleic acid comprising the nucleotide variant, wherein the nucleotide variant is a point mutation in the target nucleic acid molecule, relative to an otherwise identical target nucleic acid molecule. In some embodiments, the nucleotide variant is a non-synonymous mutation, synonymous mutation, missense mutation, nonsense mutation, non-stop mutation, or any combination thereof. In some embodiments, the point mutation is a single nucleotide polymorphism (“SNP”). In some embodiments, the detection comprises determining whether the organism is homozygous or heterozygous for the SNP. In some embodiments, determining whether the organism is homozygous or heterozygous for the SNP comprises comparing the level of the first detectable signal to the level of the second detectable signal. In some embodiments, determining whether the organism is homozygous or heterozygous for the SNP comprises identifying the organism as homozygous for the SNP if the level of the first detectable signal is about equal to the level of the second detectable signal. In some embodiments, determining whether the organism is homozygous or heterozygous for the SNP comprises identifying the organism as heterozygous for the SNP if the level of the first detectable signal is higher than the level of the second detectable signal. In some embodiments, determining whether the organism is homozygous or heterozygous for the SNP comprises identifying the organism as heterozygous for the SNP if the level of the second detectable signal is higher than the level of the first detectable signal. [0204] Various sample types comprising a target nucleic acid of interest are consistent with the present disclosure. These samples may comprise a target nucleic acid sequence for detection. In some embodiments, the detection of the target nucleic indicates an ailment, such as a disease, cancer, or genetic disorder, or genetic information, such as for phenotyping, genotyping, or determining ancestry and are compatible with the reagents and support mediums as described herein. Generally, a sample from an individual or an animal or an environmental sample may be obtained to test for presence of a disease, cancer, genetic disorder, or any mutation of interest. [0205] In some instances, the sample is a biological sample, an environmental sample, or a combination thereof. Non-limiting examples of biological samples are blood, serum, plasma, saliva, urine, mucosal sample, peritoneal sample, cerebrospinal fluid, gastric secretions, nasal secretions, sputum, pharyngeal exudates, urethral or vaginal secretions, an exudate, an effusion, and a tissue sample (e.g., a biopsy sample). A tissue sample from a subject may be dissociated or liquified prior to application to a detection system of the present disclosure. Non-limiting examples of environmental samples are soil, air, or water. In some instances, an environmental sample is taken as a swab from a surface of interest or taken directly from the surface of interest. [0206] In some instances, the sample is a raw (unprocessed, unmodified) sample. Raw samples may be applied to a system for detecting or modifying a target nucleic acid, such as those described herein. In some instances, the sample is diluted with a buffer or a fluid or concentrated prior to its application to the system or be applied neat to the detection system. Sometimes, the sample contains no more 20 µl of buffer or fluid. The sample, in some cases, is contained in no more than 1, 5, 10, 15, 20, 25, 30, 3540, 45, 50, 55, 60, 65, 70, 75, 80, 90, 100, 200, 300, 400, 500 µl, or any of value 1 µl to 500 µl, preferably 10 µL to 200 µL, or more preferably 50 µL to 100 µL of buffer or fluid. Sometimes, the sample is contained in more than 500 µl. [0207] In some instances, the sample is taken from a single-cell eukaryotic organism; a plant or a plant cell; an algal cell; a fungal cell; an animal cell, tissue, or organ; a cell, tissue, or organ from an invertebrate animal; a cell, tissue, fluid, or organ from a vertebrate animal such as fish, amphibian, reptile, bird, and mammal; a cell, tissue, fluid, or organ from a mammal such as a human, a non-human primate, an ungulate, a feline, a bovine, an ovine, and a caprine. In some instances, the sample is taken from nematodes, protozoans, helminths, or malarial parasites. In some cases, the sample comprises nucleic acids from a cell lysate from a eukaryotic cell, a mammalian cell, a human cell, a prokaryotic cell, or a plant cell. In some cases, the sample comprises nucleic acids expressed from a cell. [0208] In some instances, samples are used for diagnosing a disease. In some instances the disease is cancer. The sample used for cancer testing may comprise at least one target nucleic acid that may bind to a guide nucleic acid of the reagents described herein. The target nucleic acid, in some cases, comprises a portion of a gene comprising a mutation associated with cancer, a gene whose overexpression is associated with cancer, a tumor suppressor gene, an oncogene, a checkpoint inhibitor gene, a gene associated with cellular growth, a gene associated with cellular metabolism, or a gene associated with cell cycle. Sometimes, the target nucleic acid encodes a cancer biomarker, such as a prostate cancer biomarker or non-small cell lung cancer. In some cases, the assay may be used to detect “hotspots” in target nucleic acids that may be predictive of lung cancer. In some cases, the target nucleic acid comprises a portion of a nucleic acid that is associated with a blood fever. In some cases, the target nucleic acid is a portion of a nucleic acid from a genomic locus, any DNA amplicon of, an RNA, an in vitro transcribed RNA, a reverse transcribed mRNA, or a cDNA from a locus of at least one of: ALK, APC, ATM, AXIN2, BAP1, BARD1, BLM, BMPR1A, BRCA1, BRCA2, BRIP1, CASR, CDC73, CDH1, CDK4, CDKN1B, CDKN1C, CDKN2A, CEBPA, CHEK2, CTNNA1, DICER1, DIS3L2, EGFR, EPCAM, FH, FLCN, GATA2, GPC3, GREM1, HOXB13, HRAS, system, MAX, MEN1, MET, MITF, MLH1, MSH2, MSH3, MSH6, MUTYH, NBN, NF1, NF2, NTHL1, PALB2, PDGFRA, PHOX2B, PMS2, PNPLA3 , POLD1, POLE, POT1, PRKAR1A, PTCH1, PTEN, RAD50, RAD51C, RAD51D, RB1, RECQL4, RET, RUNX1, SDHA, SDHAF2, SDHB, SDHC, SDHD, SMAD4, SMARCA4, SMARCB1, SMARCE1, STK11, SUFU, TERC, TERT, TMEM127, TP53, TSC1, TSC2, VHL, WRN, and WT1. [0209] Any region of the aforementioned gene loci may be probed for a mutation or deletion using the compositions and methods disclosed herein. For example, in the EGFR gene locus, the compositions and methods for detection disclosed herein may be used to detect a single nucleotide polymorphism or a deletion. [0210] In some instances, samples are used to diagnose a genetic disorder, also referred to as genetic disorder testing. The sample used for genetic disorder testing may comprise at least one target nucleic acid that may bind to a guide nucleic acid of the reagents described herein. In some embodiments, the genetic disorder is hemophilia, sickle cell anemia, β-thalassemia, Duchene muscular dystrophy, severe combined immunodeficiency, Huntington’s disease, or cystic fibrosis. The target nucleic acid, in some cases, is from a gene with a mutation associated with a genetic disorder, from a gene whose overexpression is associated with a genetic disorder, from a gene associated with abnormal cellular growth resulting in a genetic disorder, or from a gene associated with abnormal cellular metabolism resulting in a genetic disorder. In some cases, the target nucleic acid is a nucleic acid from a genomic locus, a transcribed mRNA, an in vitro transcribed RNA, a reverse transcribed mRNA, a DNA amplicon of or a cDNA from a locus of at least one of: CFTR, FMR1, SMN1, ABCB11, ABCC8, ABCD1, ACAD9, ACADM, ACADVL, ACAT1, ACOX1, ACSF3, ADA, ADAMTS2, ADGRG1, AGA, AGL, AGPS, AGXT, AIRE, ALDH3A2, ALDOB, ALG6, ALMS1, ALPL, AMT, AQP2, ARG1, ARSA, ARSB, ASL, ASNS, ASPA, ASS1, ATM, ATP6V1B1, ATP7A, ATP7B, ATRX, BBS1, BBS10, BBS12, BBS2, BCKDHA, BCKDHB, BCS1L, BLM, BSND, CAPN3, CBS, CDH23, CEP290, CERKL, CHM, CHRNE, CIITA, CLN3, CLN5, CLN6, CLN8, CLRN1, CNGB3, COL27A1, COL4A3, COL4A4, COL4A5, COL7A1, CPS1, CPT1A, CPT2, CRB1, CTNS, CTSK, CYBA, CYBB, CYP11B1, CYP11B2, CYP17A1, CYP19A1, CYP27A1, DBT, DCLRE1C, DHCR7, DHDDS, DLD, DMD, DNAH5, DNAI1, DNAI2, DYSF, EDA, EIF2B5, EMD, ERCC6, ERCC8, ESCO2, ETFA, ETFDH, ETHE1, EVC, EVC2, EYS, F9, FAH, FAM161A, FANCA, FANCC, FANCG, FH, FKRP, FKTN, G6PC, GAA, GALC, GALK1, GALT, GAMT, GBA, GBE1, GCDH, GFM1, GJB1, GJB2, GLA, GLB1, GLDC, GLE1, GNE, GNPTAB, GNPTG, GNS, GRHPR, HADHA, HAX1, HBA1,, HBA2, HBB, HEXA, HEXB, HGSNAT, HLCS, HMGCL, HOGA1, HPS1, HPS3, HSD17B4, HSD3B2, HYAL1, HYLS1, IDS, IDUA, IKBKAP, IL2RG, IVD, KCNJ11, LAMA2, LAMA3, LAMB3, LAMC2, LCA5, LDLR, LDLRAP1, LHX3, LIFR, LIPA, LOXHD1, LPL, LRPPRC, MAN2B1, MCOLN1, MED17, MESP2, MFSD8, MKS1, MLC1, MMAA, MMAB, MMACHC, MMADHC, MPI, MPL, MPV17, MTHFR, MTM1, MTRR, MTTP, MUT, MYO7A, NAGLU, NAGS, NBN, NDRG1, NDUFAF5, NDUFS6, NEB, NPC1, NPC2, NPHS1, NPHS2, NR2E3, NTRK1, OAT, OPA3, OTC, PAH, PC, PCCA, PCCB, PCDH15, PDHA1, PDHB, PEX1, PEX10, PEX12, PEX2, PEX6, PEX7, PFKM, PHGDH, PKHD1, PMM2, PNPLA3, POMGNT1, PPT1, PROP1, PRPS1, PSAP, PTS, PUS1, PYGM, RAB23, RAG2, RAPSN, RARS2, RDH12, RMRP, RPE65, RPGRIP1L, RS1, RTEL1, SACS, SAMHD1, SEPSECS, SGCA, SGCB, SGCG, SGSH, SLC12A3, SLC12A6, SLC17A5, SLC22A5, SLC25A13, SLC25A15, SLC26A2, SLC26A4, SLC35A3, SLC37A4, SLC39A4, SLC4A11, SLC6A8, SLC7A7, SMARCAL1, SMPD1, STAR, SUMF1, TAT, TCIRG1, TECPR2, TFR2, TGM1, TH, TMEM216, TPP1, TRMU, TSFM, TTPA, TYMP, USH1C, USH2A, VPS13A, VPS13B, VPS45, VRK1, VSX2, WNT10A, XPA, XPC, and ZFYVE26. [0211] The sample used for phenotyping testing may comprise at least one target nucleic acid that may bind to a guide nucleic acid of the reagents described herein. The target nucleic acid, in some cases, is a nucleic acid encoding a sequence associated with a phenotypic trait. [0212] The sample used for genotyping testing may comprise at least one target nucleic acid that may bind to a guide nucleic acid of the reagents described herein. The target nucleic acid, in some cases, is a nucleic acid encoding a sequence associated with a genotype of interest. [0213] The sample used for ancestral testing may comprise at least one target nucleic acid that may bind to a guide nucleic acid of the reagents described herein. The target nucleic acid, in some cases, is a nucleic acid encoding a sequence associated with a geographic region of origin or ethnic group. [0214] The sample may be used for identifying a disease status. For example, a sample is any sample described herein, and is obtained from a subject for use in identifying a disease status of a subject. The disease may be a cancer or genetic disorder. Sometimes, a method comprises obtaining a serum sample from a subject; and identifying a disease status of the subject. Often, the disease status is prostate disease status, but the status of any disease may be assessed. [0215] Any of the above disclosed samples are consistent with the methods, compositions, reagents, enzymes, and systems disclosed herein. [0216] A number of samples are consistent with the compositions and methods disclosed herein. Described herein are samples that contain deoxyribonucleic acid (DNA), ribonucleic acid (RNA), or both, which can be detected using a programmable nuclease, such as a Type V CRISPR/Cas enzyme (e.g., a Cas12 such as Cas12 is a Cas12a, Cas12b, Cas12c, Cas12d, or Cas12e or a Cas14 such as Cas14a, Cas14b, Cas14c, Cas14d, Cas14e, Cas14f, Cas14g, or Cas14h ) or a Type VI CRISPR enzyme (e.g., a Cas13 such as Cas13a, Cas13b, Cas13c, Cas13d, or Cas13e). As described herein, programmable nucleases are activated upon binding to a target nucleic acid of interest in a sample upon hybridization of a guide nucleic acid to the target nucleic acid. Subsequently, the activated programmable nucleases exhibit sequence-independent cleavage of a nucleic acid in a reporter. The reporter additionally includes a detectable moiety, which is released upon sequence-independent cleavage of the nucleic acid in the reporter. The detectable moiety emits a detectable signal, which can be measured by various methods (e.g., spectrophotometry, fluorescence measurements, electrochemical measurements). [0217] Various sample types comprising a target nucleic acid of interest are consistent with the present disclosure. These samples can comprise a target nucleic acid sequence for detection. In some embodiments, the target nucleic is contained in a biological sample from the individual may be blood, serum, plasma, saliva, urine, mucosal sample, peritoneal sample, cerebrospinal fluid, gastric secretions, nasal secretions, sputum, pharyngeal exudates, urethral or vaginal secretions, an exudate, an effusion, or tissue. A tissue sample may be dissociated or liquified prior to application to detection system of the present disclosure. A sample from an environment may be from soil, air, or water. In some instances, the environmental sample is taken as a swab from a surface of interest or taken directly from the surface of interest. In some instances, the raw sample is applied to the detection system. In some instances, the sample is diluted with a buffer or a fluid or concentrated prior to application to the detection system or be applied neat to the detection system. Sometimes, the sample is contained in no more 20 µl. The sample, in some cases, is contained in no more than 1, 5, 10, 15, 20, 25, 30, 3540, 45, 50, 55, 60, 65, 70, 75, 80, 90, 100, 200, 300, 400, 500 µl, or any of value from 1 µl to 500 µl, preferably from 10 µL to 200 µL, or more preferably from 50 µL to 100 µL. Sometimes, the sample is contained in more than 500 µl. [0218] In some embodiments, the target nucleic acid is single-stranded DNA. The methods, reagents, enzymes, and kits disclosed herein may enable the direct detection of a DNA encoding a sequence of interest, in particular a single-stranded DNA encoding a sequence of interest, without transcribing the DNA into RNA, for example, by using an RNA polymerase. The compositions and methods disclosed herein may enable the detection of target nucleic acid that is an amplified nucleic acid of a nucleic acid of interest. In some embodiments, the target nucleic acid is a cDNA, genomic DNA, an amplicon of genomic DNA or a DNA amplicon of an RNA. A nucleic acid can encode a sequence from a genomic locus. In some cases, the target nucleic acid that binds to the guide nucleic acid is from 5 to 100, 5 to 90, 5 to 80, 5 to 70, 5 to 60, 5 to 50, 5 to 40, 5 to 30, 5 to 25, 5 to 20, 5 to 15, or 5 to 10 nucleotides in length. The nucleic acid can be from 10 to 90, from 20 to 80, from 30 to 70, or from 40 to 60 nucleotides in length. A nucleic acid can be 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 50, 60, 70, 80, 90, or 100 nucleotides in length. The target nucleic acid can encode a sequence reverse complementary to a guide nucleic acid sequence. [0219] The sample described herein may comprise at least one target nucleic acid molecule comprising a nucleotide variant at a position of interest. The sample described herein may comprise at least one target nucleic acid. The target nucleic acid as described herein comprises a segment that is reverse complementary to a segment of a guide nucleic acid. Often, the sample comprises the segment of the target nucleic acid and at least one nucleic acid comprising at least 50% sequence identity to a segment of the target nucleic acid. Sometimes, the at least one nucleic acid comprises a segment comprising at least 60%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to the segment of the target nucleic acid. Often, a sample comprises the segment of the target nucleic acid and at least one nucleic acid a segment comprising less than 100% sequence identity to the target nucleic acid but no less than 50% sequence identity to the segment of the target nucleic acid. Sometimes, a sample comprises the segment of the target nucleic acid and at least one nucleic acid a segment comprising less than 100% sequence identity to the target nucleic acid but no less than 60%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to the segment of the target nucleic acid. For example, the segment of the target nucleic acid comprises a mutation as compared to at least one nucleic acid comprising a segment comprising less than 100% sequence identity to the segment of the target nucleic acid but no less than 50% sequence identity to the segment of the target nucleic acid. Sometimes, the segment of the target nucleic acid comprises a mutation as compared to at least one nucleic acid comprising a segment comprising less than 100% sequence identity to the segment of the target nucleic acid but no less than 60%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to the segment of the target nucleic acid. Often, the segment of the target nucleic acid comprises a mutation as compared to at least one nucleic acid comprising a segment comprising less than 100% sequence identity to the segment of the target nucleic acid but no less than 50% sequence identity to the segment of the target nucleic acid. The mutation can be a mutation of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more nucleotides. Often, the mutation is a single nucleotide mutation. The single nucleotide mutation can be a single nucleotide polymorphism (SNP), which is a single base pair variation in a DNA sequence present in less than 1% of a population. Sometimes, the target nucleic acid comprises a single nucleotide mutation, wherein the single nucleotide mutation comprises the wild type variant of the SNP. The single nucleotide mutation or SNP can be associated with a phenotype of the sample or a phenotype of the organism from which the sample was taken. The SNP, in some cases, is associated with altered phenotype from wild type phenotype. Often, the segment of the target nucleic acid sequence comprises a deletion as compared to at least one nucleic acid comprising a segment comprising less than 100% sequence identity to the segment of the target nucleic acid but no less than 50% sequence identity to the segment of the target nucleic acid. The mutation can be a deletion of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more nucleotides. The mutation can be a deletion of about 5, about 10, about 15, about 20, about 25, about 30, about 35, about 40, about 45, about 50, about 55, about 60, about 65, about 70, about 75, about 80, about 85, about 90, about 95, about 100, about 200, about 300, about 400, about 500, about 600, about 700, about 800, about 900, or about 1000 nucleotides. The mutation can be a deletion of from 1 to 5, from 5 to 10, from 10 to 15, from 15 to 20, from 20 to 25, from 25 to 30, from 30 to 35, from 35 to 40, from 40 to 45, from 45 to 50, from 50 to 55, from 55 to 60, from 60 to 65, from 65 to 70, from 70 to 75, from 75 to 80, from 80 to 85, from 85 to 90, from 90 to 95, from 95 to 100, from 100 to 200, from 200 to 300, from 300 to 400, from 400 to 500, from 500 to 600, from 600 to 700, from 700 to 800, from 800 to 900, from 900 to 1000, from 1 to 50, from 1 to 100, from 25 to 50, from 25 to 100, from 50 to 100, from 100 to 500, from 100 to 1000, or from 500 to 1000 nucleotides. The segment of the target nucleic acid that the guide nucleic acid of the methods describe herein binds to comprises the mutation, such as the SNP or the deletion. The mutation can be a single nucleotide mutation or a SNP. The SNP can be a synonymous substitution or a nonsynonymous substitution. The nonsynonymous substitution can be a missense substitution or a nonsense point mutation. The mutation can be a deletion of one or more nucleotides. Often, the single nucleotide mutation, SNP, or deletion is associated with a disease such as cancer or a genetic disorder. The mutation, such as a single nucleotide mutation, a SNP, or a deletion, can be encoded in the sequence of a target nucleic acid from the germline of an organism or can be encoded in a target nucleic acid from a diseased cell, such as a cancer cell. [0220] The sample used for disease testing may comprise at least one target nucleic acid that can bind to a guide nucleic acid of the reagents described herein. The sample used for disease testing may comprise at least nucleic acid of interest that is amplified to produce a target nucleic acid that can bind to a guide nucleic acid of the reagents described herein. The nucleic acid of interest can comprise DNA, RNA, or a combination thereof. VII. Reporters [0221] The method of the present disclosure (e.g., assaying for a target nucleic acid) can comprise a reporter (also referred to herein as a reporter nucleic acid) that comprises a nucleic acid and a detectable moiety. The reporter can also be referred to as a reporter nucleic acid, wherein the reporter nucleic acid can be used to determine the presence of a target nucleic acid sequence in a sample. This section provides, in more detail, embodiments of reporter nucleic acids used in the method provided by the present disclosure. [0222] Described herein are reporter nucleic acids for detecting the presence or absence of a target nucleic acid in a sample using systems comprising an effector protein. The reporter nucleic acid can comprise a single stranded nucleic acid and a detection moiety, wherein the nucleic acid is capable of being cleaved by the activated effector protein, releasing the detection moiety, and, generating a detectable signal. The effector proteins disclosed herein, activated upon hybridization of a guide nucleic acid to a target nucleic acid, can cleave the reporter nucleic acid. Specifically, the effector proteins disclosed herein, activated upon hybridization of a gRNA to a target nucleic acid, can cleave the nucleic acid of the reporter nucleic acid. [0223] A major advantage of the compositions and methods disclosed herein is the design of excess reporter nucleic acids to total nucleic acids in an unamplified or an amplified sample, not including the nucleic acid of the reporter nucleic acid. Total nucleic acids can include the target nucleic acids and non-target nucleic acids, not including the nucleic acid of the reporter nucleic acid. The non-target nucleic acids can be from the original sample, either lysed or unlysed. The non-target nucleic acids can also be byproducts of amplification. Thus, the non- target nucleic acids can include both non-target nucleic acids from the original sample, lysed or unlysed, and from an amplified sample. The presence of a large amount of non-target nucleic acids, an activated effector protein may be inhibited in its ability to bind and cleave the reporter nucleic acid sequences. This is because the activated effector proteins collaterally cleaves any nucleic acids. If total nucleic acids are in present in large amounts, they may outcompete reporter nucleic acids for the effector proteins. The compositions and methods disclosed herein are designed to have an excess of reporter nucleic acid to total nucleic acids, such that the detectable signals from DETECTR reactions are particularly superior. In some embodiments, the reporter nucleic acid can be present in at least 1.5 fold, at least 2 fold, at least 3 fold, at least 4 fold, at least 5 fold, at least 6 fold, at least 7 fold, at least 8 fold, at least 9 fold, at least 10 fold, at least 11 fold, at least 12 fold, at least 13 fold, at least 14 fold, at least 15 fold, at least 16 fold, at least 17 fold, at least 18 fold, at least 19 fold, at least 20 fold, at least 30 fold, at least 40 fold, at least 50 fold, at least 60 fold, at least 70 fold, at least 80 fold, at least 90 fold, at least 100 fold, from 1.5 fold to 100 fold, from 2 fold to 10 fold, from 10 fold to 20 fold, from 20 fold to 30 fold, from 30 fold to 40 fold, from 40 fold to 50 fold, from 50 fold to 60 fold, from 60 fold to 70 fold, from 70 fold to 80 fold, from 80 fold to 90 fold, from 90 fold to 100 fold, from 1.5 fold to 10 fold, from 1.5 fold to 20 fold, from 10 fold to 40 fold, from 20 fold to 60 fold, or from 10 fold to 80 fold excess of total nucleic acids. [0224] A second significant advantage of the compositions and methods disclosed herein is the design of an excess volume comprising the gRNA system, the effector protein, and the reporter nucleic acid, which contacts a smaller volume comprising the sample with the target nucleic acid of interest. The smaller volume comprising the sample can be unlysed sample, lysed sample, or lysed sample which has undergone any combination of reverse transcription, amplification, and in vitro transcription. The presence of various reagents in a crude, non-lysed sample, a lysed sample, or a lysed and amplified sample, such as buffer, magnesium sulfate, salts, the pH, a reducing agent, primers, dNTPs, NTPs, cellular lysates, non-target nucleic acids, primers, or other components, can inhibit the ability of the effector protein to become activated or to find and cleave the nucleic acid of the reporter nucleic acid. This may be due to nucleic acids that are not the reporter nucleic acid outcompeting the nucleic acid of the reporter nucleic acid, for the effector protein. Alternatively, various reagents in the sample may simply inhibit the activity of the effector protein. Thus, the compositions and methods provided herein for contacting an excess volume comprising the gRNA system, the effector protein, and the reporter nucleic acid to a smaller volume comprising the sample with the target nucleic acid of interest provides for superior detection of the target nucleic acid by ensuring that the effector protein is able to find and cleaves the nucleic acid of the reporter nucleic acid. In some embodiments, the volume comprising the gRNA system, the effector protein, and the reporter nucleic acid (can be referred to as “a second volume”) is 4-fold greater than a volume comprising the sample (can be referred to as “a first volume”). In some embodiments, the volume comprising the gRNA system, the effector protein, and the reporter nucleic acid (can be referred to as “a second volume”) is at least 1.5 fold, at least 2 fold, at least 3 fold, at least 4 fold, at least 5 fold, at least 6 fold, at least 7 fold, at least 8 fold, at least 9 fold, at least 10 fold, at least 11 fold, at least 12 fold, at least 13 fold, at least 14 fold, at least 15 fold, at least 16 fold, at least 17 fold, at least 18 fold, at least 19 fold, at least 20 fold, at least 30 fold, at least 40 fold, at least 50 fold, at least 60 fold, at least 70 fold, at least 80 fold, at least 90 fold, at least 100 fold, from 1.5 fold to 100 fold, from 2 fold to 10 fold, from 10 fold to 20 fold, from 20 fold to 30 fold, from 30 fold to 40 fold, from 40 fold to 50 fold, from 50 fold to 60 fold, from 60 fold to 70 fold, from 70 fold to 80 fold, from 80 fold to 90 fold, from 90 fold to 100 fold, from 1.5 fold to 10 fold, from 1.5 fold to 20 fold, from 10 fold to 40 fold, from 20 fold to 60 fold, or from 10 fold to 80 fold greater than a volume comprising the sample (can be referred to as “a first volume”). In some embodiments, the volume comprising the sample is at least 0.5 µL, at least 1 µL, at least at least 1 µL, at least 2 µL, at least 3 µL, at least 4 µL, at least 5 µL, at least 6 µL, at least 7 µL, at least 8 µL, at least 9 µL, at least 10 µL, at least 11 µL, at least 12 µL, at least 13 µL, at least 14 µL, at least 15 µL, at least 16 µL, at least 17 µL, at least 18 µL, at least 19 µL, at least 20 µL, at least 25 µL, at least 30 µL, at least 35 µL, at least 40 µL, at least 45 µL, at least 50 µL, at least 55 µL, at least 60 µL, at least 65 µL, at least 70 µL, at least 75 µL, at least 80 µL, at least 85 µL, at least 90 µL, at least 95 µL, at least 100 µL, from 0.5 µL to 5 µL µL, from 5 µL to 10 µL, from 10 µL to 15 µL, from 15 µL to 20 µL, from 20 µL to 25 µL, from 25 µL to 30 µL, from 30 µL to 35 µL, from 35 µL to 40 µL, from 40 µL to 45 µL, from 45 µL to 50 µL, from 10 µL to 20 µL, from 5 µL to 20 µL, from 1 µL to 40 µL, from 2 µL to 10 µL, or from 1 µL to 10 µL. In some embodiments, the volume comprising the effector protein, the gRNA system, and the reporter nucleic acid is at least 10 µL, at least 11 µL, at least 12 µL, at least 13 µL, at least 14 µL, at least 15 µL, at least 16 µL, at least 17 µL, at least 18 µL, at least 19 µL, at least 20 µL, at least 21 µL, at least 22 µL, at least 23 µL, at least 24 µL, at least 25 µL, at least 26 µL, at least 27 µL, at least 28 µL, at least 29 µL, at least 30 µL, at least 40 µL, at least 50 µL, at least 60 µL, at least 70 µL, at least 80 µL, at least 90 µL, at least 100 µL, at least 150 µL, at least 200 µL, at least 250 µL, at least 300 µL, at least 350 µL, at least 400 µL, at least 450 µL, at least 500 µL, from 10 µL to 15 µL µL, from 15 µL to 20 µL, from 20 µL to 25 µL, from 25 µL to 30 µL, from 30 µL to 35 µL, from 35 µL to 40 µL, from 40 µL to 45 µL, from 45 µL to 50 µL, from 50 µL to 55 µL, from 55 µL to 60 µL, from 60 µL to 65 µL, from 65 µL to 70 µL, from 70 µL to 75 µL, from 75 µL to 80 µL, from 80 µL to 85 µL, from 85 µL to 90 µL, from 90 µL to 95 µL, from 95 µL to 100 µL, from 100 µL to 150 µL, from 150 µL to 200 µL, from 200 µL to 250 µL, from 250 µL to 300 µL, from 300 µL to 350 µL, from 350 µL to 400 µL, from 400 µL to 450 µL, from 450 µL to 500 µL, from 10 µL to 20 µL, from 10 µL to 30 µL, from 25 µL to 35 µL, from 10 µL to 40 µL, from 20 µL to 50 µL, from 18 µL to 28 µL, or from 17 µL to 22 µL. [0225] The nucleic acid of a reporter nucleic acid can be a single-stranded nucleic acid sequence comprising at least one deoxyribonucleotide and at least one ribonucleotide. In some cases, the nucleic acid of a reporter nucleic acid is a single-stranded nucleic acid comprising at least one ribonucleotide residue at an internal position that functions as a cleavage site. In some cases, the nucleic acid of a reporter nucleic acid comprises at least 2, 3, 4, 5, 6, 7, 8, 9, or 10 ribonucleotide residues at an internal position. In some cases, the nucleic acid of a reporter nucleic acid comprises from 2 to 10, from 3 to 9, from 4 to 8, or from 5 to 7 ribonucleotide residues at an internal position. Sometimes the ribonucleotide residues are continuous. Alternatively, the ribonucleotide residues are interspersed in between non-ribonucleotide residues. In some cases, the nucleic acid of a reporter nucleic acid has only ribonucleotide residues. In some cases, the nucleic acid of a reporter nucleic acid has only deoxyribonucleotide residues. In some cases, the nucleic acid comprises nucleotides resistant to cleavage by the effector protein described herein. In some cases, the nucleic acid of a reporter nucleic acid comprises synthetic nucleotides. In some cases, the nucleic acid of a reporter nucleic acid comprises at least one ribonucleotide residue and at least one non-ribonucleotide residue. In some cases, the nucleic acid of a reporter nucleic acid is 5-20, 5-15, 5-10, 7-20, 7-15, or 7-10 nucleotides in length. In some cases, the nucleic acid of a reporter nucleic acid is from 3 to 20, from 4 to 10, from 5 to 10, or from 5 to 8 nucleotides in length. In some cases, the nucleic acid of a reporter nucleic acid comprises at least one uracil ribonucleotide. In some cases, the nucleic acid of a reporter nucleic acid comprises at least two uracil ribonucleotides. Sometimes the nucleic acid of a reporter nucleic acid has only uracil ribonucleotides. In some cases, the nucleic acid of a reporter nucleic acid comprises at least one adenine ribonucleotide. In some cases, the nucleic acid of a reporter nucleic acid comprises at least two adenine ribonucleotide. In some cases, the nucleic acid of a reporter nucleic acid has only adenine ribonucleotides. In some cases, the nucleic acid of a reporter nucleic acid comprises at least one cytosine ribonucleotide. In some cases, the nucleic acid of a reporter nucleic acid comprises at least two cytosine ribonucleotide. In some cases, the nucleic acid of a reporter nucleic acid comprises at least one guanine ribonucleotide. In some cases, the nucleic acid of a reporter nucleic acid comprises at least two guanine ribonucleotide. A nucleic acid of a reporter nucleic acid can comprise only unmodified ribonucleotides, only unmodified deoxyribonucleotides, or a combination thereof. In some cases, the nucleic acid of a reporter nucleic acid is from 5 to 12 nucleotides in length. In some cases, the nucleic acid of a reporter nucleic acid is at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides in length. In some cases, the nucleic acid of a reporter nucleic acid is 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides in length. For cleavage by an effector protein comprising Cas12, a nucleic acid of a reporter nucleic acid can be 10 nucleotides in length. [0226] The single stranded nucleic acid of a reporter nucleic acid comprises a detection moiety capable of generating a first detectable signal. Sometimes the reporter nucleic acid comprises a protein capable of generating a signal. A signal can be a calorimetric, potentiometric, amperometric, optical (e.g., fluorescent, colorimetric, etc.), or piezo-electric signal. In some cases, a detection moiety is on one side of the cleavage site. Optionally, a quenching moiety is on the other side of the cleavage site. Sometimes the quenching moiety is a fluorescence quenching moiety. In some cases, the quenching moiety is 5’ to the cleavage site and the detection moiety is 3’ to the cleavage site. In some cases, the detection moiety is 5’ to the cleavage site and the quenching moiety is 3’ to the cleavage site. Sometimes the quenching moiety is at the 5’ terminus of the nucleic acid of a reporter nucleic acid. Sometimes the detection moiety is at the 3’ terminus of the nucleic acid of a reporter nucleic acid. In some cases, the detection moiety is at the 5’ terminus of the nucleic acid of a reporter nucleic acid. In some cases, the quenching moiety is at the 3’ terminus of the nucleic acid of a reporter nucleic acid. In some cases, the single-stranded nucleic acid of a reporter nucleic acid is at least one population of the single-stranded nucleic acid capable of generating a first detectable signal. In some cases, the single-stranded nucleic acid of a reporter nucleic acid is a population of the single stranded nucleic acid capable of generating a first detectable signal. Optionally, there is more than one population of single-stranded nucleic acid of a reporter nucleic acid. In some cases, there are 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 30, 40, 50, or greater than 50, or any number spanned by the range of this list of different populations of single-stranded nucleic acids of a reporter nucleic acid capable of generating a detectable signal. In some cases, there are from 2 to 50, from 3 to 40, from 4 to 30, from 5 to 20, or from 6 to 10 different populations of single-stranded nucleic acids of a reporter nucleic acid capable of generating a detectable signal. TABLE 5 – Exemplary Single Stranded Nucleic Acids in a Reporter Nucleic Acid

/56-FAM/: 5′ 6-Fluorescein (Integrated DNA Technologies) /3IABkFQ/: 3′ Iowa Black FQ (Integrated DNA Technologies) /5IRD700/: 5′ IRDye 700 (Integrated DNA Technologies) /5TYE665/: 5′ TYE 665 (Integrated DNA Technologies) /5Alex594N/: 5′ Alexa Fluor 594 (NHS Ester) (Integrated DNA Technologies) /5ATTO633N/: 5′ ATTO TM 633 (NHS Ester) (Integrated DNA Technologies) /3IRQC1N/: 3′ IRDye QC-1 Quencher (Li-Cor) /3IAbRQSp/: 3′ Iowa Black RQ (Integrated DNA Technologies) rU: uracil ribonucleotide rG: guanine ribonucleotide *This Table refers to the detection moiety and quencher moiety as their tradenames and their source is identified. However, alternatives, generics, or non-tradename moieties with similar function from other sources can also be used. [0227] A detection moiety can be an infrared fluorophore. A detection moiety can be a fluorophore that emits fluorescence in the range of from 500 nm and 720 nm. A detection moiety can be a fluorophore that emits fluorescence in the range of from 500 nm and 720 nm. In some cases, the detection moiety emits fluorescence at a wavelength of 700 nm or higher. In other cases, the detection moiety emits fluorescence at about 660 nm or about 670 nm. In some cases, the detection moiety emits fluorescence in the range of from 500 to 520, 500 to 540, 500 to 590, 590 to 600, 600 to 610, 610 to 620, 620 to 630, 630 to 640, 640 to 650, 650 to 660, 660 to 670, 670 to 680, 690 to 690, 690 to 700, 700 to 710, 710 to 720, or 720 to 730 nm. In some cases, the detection moiety emits fluorescence in the range from 450 nm to 750 nm, from 500 nm to 650 nm, or from 550 to 650 nm. A detection moiety can be a fluorophore that emits a detectable fluorescence signal in the same range as 6-Fluorescein, IRDye 700, TYE 665, Alex Fluor, or ATTO TM 633 (NHS Ester). A detection moiety can be fluorescein amidite, 6-Fluorescein, IRDye 700, TYE 665, Alex Fluor 594, or ATTO TM 633 (NHS Ester). A detection moiety can be a fluorophore that emits a fluorescence in the same range as 6-Fluorescein (Integrated DNA Technologies), IRDye 700 (Integrated DNA Technologies), TYE 665 (Integrated DNA Technologies), Alex Fluor 594 (Integrated DNA Technologies), or ATTO TM 633 (NHS Ester) (Integrated DNA Technologies). A detection moiety can be fluorescein amidite, 6-Fluorescein (Integrated DNA Technologies), IRDye 700 (Integrated DNA Technologies), TYE 665 (Integrated DNA Technologies), Alex Fluor 594 (Integrated DNA Technologies), or ATTO TM 633 (NHS Ester) (Integrated DNA Technologies). Any of the detection moieties described herein can be from any commercially available source, can be an alternative with a similar function, a generic, or a non-tradename of the detection moieties listed. [0228] A detection moiety can be chosen for use based on the type of sample to be tested. For example, a detection moiety that is an infrared fluorophore is used with a urine sample. As another example, SEQ ID NO: 367 with a fluorophore that emits a fluorescence around 520 nm is used for testing in non-urine samples, and SEQ ID NO: 373 with a fluorophore that emits a fluorescence around 700 nm is used for testing in urine samples. [0229] A quenching moiety can be chosen based on its ability to quench the detection moiety. A quenching moiety can be a non-fluorescent fluorescence quencher. A quenching moiety can quench a detection moiety that emits fluorescence in the range of from 500 nm and 720 nm. A quenching moiety can quench a detection moiety that emits fluorescence in the range of from 500 nm and 720 nm. In some cases, the quenching moiety quenches a detection moiety that emits fluorescence at a wavelength of 700 nm or higher. In other cases, the quenching moiety quenches a detection moiety that emits fluorescence at about 660 nm or about 670 nm. In some cases, the quenching moiety quenches a detection moiety that emits fluorescence in the range of from 500 to 520, 500 to 540, 500 to 590, 590 to 600, 600 to 610, 610 to 620, 620 to 630, 630 to 640, 640 to 650, 650 to 660, 660 to 670, 670 to 680, 690 to 690, 690 to 700, 700 to 710, 710 to 720, or 720 to 730 nm. In some cases, the quenching moiety quenches a detection moiety that emits fluorescence in the range from 450 nm to 750 nm, from 500 nm to 650 nm, or from 550 to 650 nm. A quenching moiety can quench fluorescein amidite, 6-Fluorescein, IRDye 700, TYE 665, Alex Fluor 594, or ATTO TM 633 (NHS Ester). A quenching moiety can be Iowa Black RQ, Iowa Black FQ or IRDye QC-1 Quencher. A quenching moiety can quench fluorescein amidite, 6-Fluorescein (Integrated DNA Technologies), IRDye 700 (Integrated DNA Technologies), TYE 665 (Integrated DNA Technologies), Alex Fluor 594 (Integrated DNA Technologies), or ATTO TM 633 (NHS Ester) (Integrated DNA Technologies). A quenching moiety can be Iowa Black RQ (Integrated DNA Technologies), Iowa Black FQ (Integrated DNA Technologies) or IRDye QC-1 Quencher (LiCor). Any of the quenching moieties described herein can be from any commercially available source, can be an alternative with a similar function, a generic, or a non-tradename of the quenching moieties listed. [0230] The generation of the detectable signal from the release of the detection moiety indicates that cleavage by the effector protein has occurred and that the sample contains the target nucleic acid. In some cases, the detection moiety comprises a fluorescent dye. Sometimes the detection moiety comprises a fluorescence resonance energy transfer (FRET) pair. In some cases, the detection moiety comprises an infrared (IR) dye. In some cases, the detection moiety comprises an ultraviolet (UV) dye. Alternatively or in combination, the detection moiety comprises a polypeptide. Sometimes the detection moiety comprises a biotin. Sometimes the detection moiety comprises at least one of avidin or streptavidin. In some instances, the detection moiety comprises a polysaccharide, a polymer, or a nanoparticle. In some instances, the detection moiety comprises a gold nanoparticle or a latex nanoparticle. [0231] A detection moiety can be any moiety capable of generating a calorimetric, potentiometric, amperometric, optical (e.g., fluorescent, colorimetric, etc.), or piezo-electric signal. A nucleic acid of a reporter nucleic acid, sometimes, is protein-nucleic acid that is capable of generating a calorimetric, potentiometric, amperometric, optical (e.g., fluorescent, colorimetric, etc.), or piezo-electric signal upon cleavage of the nucleic acid. Often a calorimetric signal is heat produced after cleavage of the nucleic acids of a reporter nucleic acid. Sometimes, a calorimetric signal is heat absorbed after cleavage of the nucleic acids of a reporter nucleic acid. A potentiometric signal, for example, is electrical potential produced after cleavage of the nucleic acids of a reporter nucleic acid. An amperometric signal can be movement of electrons produced after the cleavage of nucleic acid of a reporter nucleic acid. Often, the signal is an optical signal, such as a colorimetric signal or a fluorescence signal. An optical signal is, for example, a light output produced after the cleavage of the nucleic acids of a reporter nucleic acid. Sometimes, an optical signal is a change in light absorbance between before and after the cleavage of nucleic acids of a reporter nucleic acid. Often, a piezo-electric signal is a change in mass between before and after the cleavage of the nucleic acid of a reporter nucleic acid. [0232] Often, the protein-nucleic acid is an enzyme-nucleic acid. The enzyme may be sterically hindered when present as in the enzyme-nucleic acid, but then functional upon cleavage from the nucleic acid. Often, the enzyme is an enzyme that produces a reaction with a substrate. An enzyme can be invertase. Often, the substrate of invertase is sucrose. A DNS reagent produces a colorimetric change when invertase converts sucrose to glucose. In some cases, it is preferred that the nucleic acid (e.g., DNA) and invertase are conjugated using a heterobifunctional linker via sulfo-SMCC chemistry. Sometimes the protein-nucleic acid is a substrate-nucleic acid. Often the substrate is a substrate that produces a reaction with an enzyme. [0233] A protein-nucleic acid may be attached to a solid support. The solid support, for example, is a surface. A surface can be an electrode. Sometimes the solid support is a bead. Often the bead is a magnetic bead. Upon cleavage, the protein is liberated from the solid and interacts with other mixtures. For example, the protein is an enzyme, and upon cleavage of the nucleic acid of the enzyme-nucleic acid, the enzyme flows through a chamber into a mixture comprising the substrate. When the enzyme meets the enzyme substrate, a reaction occurs, such as a colorimetric reaction, which is then detected. As another example, the protein is an enzyme substrate, and upon cleavage of the nucleic acid of the enzyme substrate-nucleic acid, the enzyme flows through a chamber into a mixture comprising the enzyme. When the enzyme substrate meets the enzyme, a reaction occurs, such as a calorimetric reaction, which is then detected. [0234] Often, the signal is a colorimetric signal or a signal visible by eye. In some instances, the signal is fluorescent, electrical, chemical, electrochemical, or magnetic. A signal can be a calorimetric, potentiometric, amperometric, optical (e.g., fluorescent, colorimetric, etc.), or piezo-electric signal. In some cases, the detectable signal is a colorimetric signal or a signal visible by eye. In some instances, the detectable signal is fluorescent, electrical, chemical, electrochemical, or magnetic. In some cases, the first detection signal is generated by binding of the detection moiety to the capture molecule in the detection region, where the first detection signal indicates that the sample contained the target nucleic acid. Sometimes the system is capable of detecting more than one type of target nucleic acid, wherein the system comprises more than one type of gRNA system (e.g., discretegRNA system or composite gRNA) and more than one type of nucleic acid of a reporter nucleic acid. In some cases, the detectable signal is generated directly by the cleavage event. Alternatively or in combination, the detectable signal is generated indirectly by the signal event. Sometimes the detectable signal is not a fluorescent signal. In some instances, the detectable signal is a colorimetric or color-based signal. In some cases, the detected target nucleic acid is identified based on its spatial location on the detection region of the support medium. In some cases, the second detectable signal is generated in a spatially distinct location than the first generated signal. [0235] In some cases, the threshold of detection, for a subject method of detecting a single stranded target nucleic acid in a sample, is less than or equal to 10 nM. The term "threshold of detection" is used herein to describe the minimal amount of target nucleic acid that must be present in a sample in order for detection to occur. For example, when a threshold of detection is 10 nM, then a signal can be detected when a target nucleic acid is present in the sample at a concentration of 10 nM or more. In some cases, the threshold of detection is less than or equal to 5 nM, 1 nM, 0.5 nM, 0.1 nM, 0.05 nM, 0.01 nM, 0.005 nM, 0.001 nM, 0.0005 nM, 0.0001 nM, 0.00005 nM, 0.00001 nM, 10 pM, 1 pM, 500 fM, 250 fM, 100 fM, 50 fM, 10 fM, 5 fM, 1 fM, 500 attomole (aM), 100 aM, 50 aM, 10 aM, or 1 aM. In some cases, the threshold of detection is in a range of from 1 aM to 1 nM, 1 aM to 500 pM, 1 aM to 200 pM, 1 aM to 100 pM, 1 aM to 10 pM, 1 aM to 1 pM, 1 aM to 500 fM, 1 aM to 100 fM, 1 aM to 1 fM, 1 aM to 500 aM, 1 aM to 100 aM, 1 aM to 50 aM, 1 aM to 10 aM, 10 aM to 1 nM, 10 aM to 500 pM, 10 aM to 200 pM, 10 aM to 100 pM, 10 aM to 10 pM, 10 aM to 1 pM, 10 aM to 500 fM, 10 aM to 100 fM, 10 aM to 1 fM, 10 aM to 500 aM, 10 aM to 100 aM, 10 aM to 50 aM, 100 aM to 1 nM, 100 aM to 500 pM, 100 aM to 200 pM, 100 aM to 100 pM, 100 aM to 10 pM, 100 aM to 1 pM, 100 aM to 500 fM, 100 aM to 100 fM, 100 aM to 1 fM, 100 aM to 500 aM, 500 aM to 1 nM, 500 aM to 500 pM, 500 aM to 200 pM, 500 aM to 100 pM, 500 aM to 10 pM, 500 aM to 1 pM, 500 aM to 500 fM, 500 aM to 100 fM, 500 aM to 1 fM, 1 fM to 1 nM, 1 fM to 500 pM, 1 fM to 200 pM, 1 fM to 100 pM, 1 fM to 10 pM, 1 fM to 1 pM, 10 fM to 1 nM, 10 fM to 500 pM, 10 fM to 200 pM, 10 fM to 100 pM, 10 fM to 10 pM, 10 fM to 1 pM, 500 fM to 1 nM, 500 fM to 500 pM, 500 fM to 200 pM, 500 fM to 100 pM, 500 fM to 10 pM, 500 fM to 1 pM, 800 fM to 1 nM, 800 fM to 500 pM, 800 fM to 200 pM, 800 fM to 100 pM, 800 fM to 10 pM, 800 fM to 1 pM, fom 1 pM to 1 nM, 1 pM to 500 pM, 1 pM to 200 pM, 1 pM to 100 pM, or 1 pM to 10 pM. In some cases, the threshold of detection in a range of from 800 fM to 100 pM, 1 pM to 10 pM, 10 fM to 500 fM, 10 fM to 50 fM, 50 fM to 100 fM, 100 fM to 250 fM, or 250 fM to 500 fM. In some cases the threshold of detection is in a range of from 2 aM to 100 pM, from 20 aM to 50 pM, from 50 aM to 20 pM, from 200 aM to 5 pM, or from 500 aM to 2 pM. In some cases, the minimum concentration at which a single stranded target nucleic acid is detected in a sample is in a range of from 1 aM to 1 nM, 10 aM to 1 nM, 100 aM to 1 nM, 500 aM to 1 nM, 1 fM to 1 nM, 1 fM to 500 pM, 1 fM to 200 pM, 1 fM to 100 pM, 1 fM to 10 pM, 1 fM to 1 pM, 10 fM to 1 nM, 10 fM to 500 pM, 10 fM to 200 pM, 10 fM to 100 pM, 10 fM to 10 pM, 10 fM to 1 pM, 500 fM to 1 nM, 500 fM to 500 pM, 500 fM to 200 pM, 500 fM to 100 pM, 500 fM to 10 pM, 500 fM to 1 pM, 800 fM to 1 nM, 800 fM to 500 pM, 800 fM to 200 pM, 800 fM to 100 pM, 800 fM to 10 pM, 800 fM to 1 pM, 1 pM to 1 nM, 1 pM to 500 pM, from 1 pM to 200 pM, 1 pM to 100 pM, or 1 pM to 10 pM. In some cases, the minimum concentration at which a single stranded target nucleic acid is detected in a sample is in a range of from 2 aM to 100 pM, from 20 aM to 50 pM, from 50 aM to 20 pM, from 200 aM to 5 pM, or from 500 aM to 2 pM. In some cases, the minimum concentration at which a single stranded target nucleic acid can be detected in a sample is in a range of from 1 aM to 100 pM. In some cases, the minimum concentration at which a single stranded target nucleic acid can be detected in a sample is in a range of from 1 fM to 100 pM. In some cases, the minimum concentration at which a single stranded target nucleic acid can be detected in a sample is in a range of from 10 fM to 100 pM. In some cases, the minimum concentration at which a single stranded target nucleic acid can be detected in a sample is in a range of from 800 fM to 100 pM. In some cases, the minimum concentration at which a single stranded target nucleic acid can be detected in a sample is in a range of from 1 pM to 10 pM. In some cases, the devices, systems, fluidic devices, kits, and methods described herein detect a target single-stranded nucleic acid in a sample comprising a plurality of nucleic acids such as a plurality of non-target nucleic acids, where the target single-stranded nucleic acid is present at a concentration as low as 1 aM, 10 aM, 100 aM, 500 aM, 1 fM, 10 fM, 500 fM, 800 fM, 1 pM, 10 pM, 100 pM, or 1 pM. ILLUSTRATIVE EMBODIMENTS [0236] The present disclosure provides the following illustrative embodiments. [0237] Embodiment 1: A method of assaying for a target nucleic acid comprising a nucleotide variant at a position of interest, the method comprising: a. contacting a sample to: i. a composition comprising an effector protein and a guide nucleic acid; and ii. a reporter, and b. detecting a presence or absence of a target nucleic acid comprising the nucleotide variant in the sample by assaying for a signal indicative of cleavage of the reporter by the effector protein; wherein the detecting comprises comparing the signal to a control signal produced by contacting the composition and reporter to a control nucleic acid molecule not comprising the nucleotide variant, but that is otherwise identical to the target nucleic acid, at least apart from a variation of less than twenty nucleotides. [0238] Embodiment 2: The method of Embodiment 1, wherein assaying for a signal produced by the effector protein comprises assaying for a signal, or change in signal, produced by trans cleavage of the reporter by the effector protein, wherein the trans cleavage is activated upon hybridization of the guide nucleic acid to the target nucleic acid molecule comprising the nucleotide variant [0239] Embodiment 3: The method of Embodiment 1, wherein the control nucleic acid molecule is otherwise identical to the target nucleic acid molecule, apart from a variation of less than four nucleotides. [0240] Embodiment 4: The method of Embodiment 1, wherein the control nucleic acid molecule is otherwise identical to the target nucleic acid molecule, apart from a variation of less than two nucleotides. [0241] Embodiment 5: The method of Embodiment 1, wherein the control nucleic acid molecule is otherwise identical to the target nucleic acid molecule. [0242] Embodiment 6: The method of Embodiment 1, wherein the nucleotide variant is a point mutation in the target nucleic acid molecule, relative to an otherwise identical target nucleic acid molecule. [0243] Embodiment 7: The method of Embodiment 1 or 2, wherein the nucleotide variant is a non-synonymous mutation. [0244] Embodiment 8: The method of any one of Embodiments 1-7, wherein the nucleotide variant is a synonymous mutation. [0245] Embodiment 9: The method of any one of Embodiments 1-7, wherein the nucleotide variant is a missense mutation, a nonsense mutation, or a non-stop mutation. [0246] Embodiment 10: The method of any one of Embodiments 2-9, wherein the point mutation is a single nucleotide polymorphism (“SNP”). [0247] Embodiment 11: The method of any one of Embodiments 1-10, wherein the nucleotide variant is associated with a disease. [0248] Embodiment 12: The method of Embodiment 11, wherein the disease is a cancer, an inherited disorder, an ophthalmological disorder, an endocrinological disorder, an autoimmune disorder, a metabolic disorder, or a combination thereof. [0249] Embodiment 13: The method of Embodiment 12, wherein the metabolic disorder is nonalcoholic fatty liver disease, alcoholic liver disease, liver disease, hepatitis, chronic hepatitis, hepatocellular carcinoma, diabetes, cirrhosis, steatosis, fibrosis, obesity, or a combination thereof. [0250] Embodiment 14: The method of Embodiment 13, wherein the metabolic disorder is liver disease. [0251] Embodiment 15: The method of Embodiment 11, wherein the disease is selected from a group consisting of: asthma, arrhythmia, blood pressure, biliary cirrhosis, bipolar affective disorder, colorectal cancer, Crohn’s Disease, dyslipidemia, eating disorder, esophageal adenocarcinoma, hyperbilirubinemia, idiopathic arthritis, idiopathic PD and FTD, knee and hip osteoarthritis, lung cancer, myocardial infraction, migraine, obesity, ossification, oxalate stone, POAG, rheumatoid arthritis, systemic sclerosis, severe sepsis, Type II diabetes, ulcerative colitis, urinary bladder cancer, and autism. [0252] Embodiment 16: The method of any one of Embodiments 1-15, wherein the target nucleic acid is, or is encoded by, a gene selected from a group consisting of: EDN1, NOS1, KCN1, TAF1, MBL, HRT 3A, Cyclin D1, UGT1A1 UDP, MIF, SNCA, LRRK2, MMP1, PAI, PAI1, Npps, CDH, CDH1, POAG, TNF, TNF-α, MDR1, TSP, PCS, PNPLA3, IR, INSR, CNP, LPL, MCR, MC1R, TMEM, C9ORF72, MAPT, GRN, COL, p53, MYOC, FBN1, STX1A, CCN, CCND1 cyclin D1, a fragment thereof, or any combination thereof. [0253] Embodiment 17: The method of any one of Embodiments 1-16, wherein the target nucleic acid is, or is encoded by, a PNPLA3 gene or a fragment thereof. [0254] Embodiment 18: The method of any one of Embodiments 1-17, wherein the target nucleic acid is a fragment of a PNPLA3 gene. [0255] Embodiment 19: The method of Embodiment 17 or 18, wherein the PNPLA3 gene comprises a substitution of a C with a G at nucleotide position 444 of SEQ ID NO: 384. [0256] Embodiment 20: The method of any one of Embodiments 17-19, wherein the PNPLA3 gene encodes a PNPLA3 protein comprising an I to M substitution at amino acid position of 148 of SEQ ID NO: 385. [0257] Embodiment 21: The method of any one of Embodiments 1-20, wherein the nucleotide variant is an SNP, a marker of a disease, or a combination thereof. [0258] Embodiment 22: The method of Embodiment 21, comprising determining whether an organism from which the sample is derived is homozygous for the nucleotide variant. [0259] Embodiment 23: The method of Embodiment 21 or 22, comprising determining whether an organism from which the sample is derived is heterozygous for the nucleotide variant. [0260] Embodiment 24: The method of any one of Embodiments 1-23, wherein the effector protein is a Type V or Type VI Cas effector protein. [0261] Embodiment 25: The method of Embodiment 24, wherein the type V Cas effector protein is a Cas12 protein. [0262] Embodiment 26: The method of Embodiment 25, wherein the Cas12 protein comprises a Cas12a polypeptide, a Cas12b polypeptide, a Cas12c polypeptide, a Cas12d polypeptide, a Cas12e polypeptide, a C2c4 polypeptide, a C2c8 polypeptide, a C2c5 polypeptide, a C2c10 polypeptide, or a C2c9 polypeptide. [0263] Embodiment 27: The method of any one of Embodiments 25-26, wherein the Cas12 protein is at least 80% identical to SEQ ID NO: 11. [0264] Embodiment 28: The method of any one of Embodiments 25-27, wherein the Cas12 protein is at least 95% identical to SEQ ID NO: 11. [0265] Embodiment 29: The method of any one of Embodiments 25-28, wherein the Cas12 protein is SEQ ID NO: 11. [0266] Embodiment 30: The method of Embodiment 24, wherein the type V Cas effector protein is a Cas14 protein. [0267] Embodiment 31: The method of Embodiment 30, wherein the Cas14 protein comprises a Cas14a polypeptide, a Cas14b polypeptide, a Cas14c polypeptide, a Cas14d polypeptide, a Cas14e polypeptide, a Cas14f polypeptide, a Cas14g polypeptide, a Cas14h polypeptide, a Cas14i polypeptide, a Cas14j polypeptide, or a Cas14k polypeptide. [0268] Embodiment 32: The method of Embodiment 24, wherein the type V Cas effector protein is a CasФ protein. [0269] Embodiment 33: The method of Embodiment 24, wherein the type VI Cas effector protein is a Cas13 protein. [0270] Embodiment 34: The method of Embodiment 33, wherein the Cas13 protein comprises a Cas13a polypeptide, a Cas13b polypeptide, a Cas13c polypeptide, a Cas13c polypeptide, a Cas13d polypeptide, or a Cas13e polypeptide. [0271] Embodiment 35: The method of any one of Embodiments 1-34, wherein the reporter comprises a fluorophore, a quencher, or a combination thereof. [0272] Embodiment 36: The method of any one of Embodiments 1-35, wherein the reporter comprises a fluorescence resonance energy transfer (FRET) pair. [0273] Embodiment 37: The method of any one of Embodiments 1-36, wherein the target nucleic acid is DNA. [0274] Embodiment 38: The method of Embodiment 37, wherein the DNA is single or double stranded DNA. [0275] Embodiment 39: The method of Embodiment 37 or 38, wherein the DNA is purified genomic DNA. [0276] Embodiment 40: The method of Embodiment 37 or 38, wherein the DNA is pre- amplified DNA. [0277] Embodiment 41: The method of any one of Embodiments 1-36, wherein the target nucleic acid is RNA. [0278] Embodiment 42: The method of Embodiment 41, wherein the RNA is double stranded or single stranded RNA. [0279] Embodiment 43: The method of Embodiment 41 or 42, wherein the RNA is purified genomic RNA. [0280] Embodiment 44: The method of Embodiment 41 or 42, wherein the RNA is pre- amplified RNA. [0281] Embodiment 45: The method of any one of Embodiments 1-44, wherein the sample is suspended in a buffer composition. [0282] Embodiment 46: The method of any one of Embodiments 1-45, wherein the sample is suspended in a buffer composition with a pH of about 7 to about 9. [0283] Embodiment 47: The method of any one of Embodiments 1-46, wherein the sample is suspended in a buffer composition that enhances DNA detection. [0284] Embodiment 48: The method of any one of Embodiments 1-47, wherein the sample comprises at most 250 target nucleic acid copies per assay. [0285] Embodiment 49: The method of any one of Embodiments 1-48, wherein the sample is derived from an organism selected from the group consisting of: unicellular organisms, multicellular organisms, pathogenic organisms, living organisms, or any combination thereof. [0286] Embodiment 50: The method of Embodiment 49, wherein the living organism is a human, an animal, a plant, a crop, or any combination thereof. [0287] Embodiment 51: The method of Embodiment 46, wherein the Cas12 protein associates with a gRNA comprising a nucleotide sequence that is at least 75% identical to any one of SEQ ID NOs: 209-366. [0288] Embodiment 52: The method of Embodiment 46, wherein the Cas12 protein associates with a gRNA comprising a nucleotide sequence that is at least 95% identical to any one of SEQ ID NOs: 209-366. [0289] Embodiment 53: The method of Embodiment 46, wherein the Cas12 protein associates with a gRNA comprising a nucleotide sequence that is at least 100% identical to any one of SEQ ID NOs: 209-366. [0290] Embodiment 54: A method for determining a variant genotype in an organism, comprising: a. assaying for at least one target nucleic acid comprising a genomic variant in a sample by assaying for a first signal indicative of activity of a first effector protein; b. assaying for at least one target nucleic acid not comprising the genomic variant in the sample by assaying for a second signal indicative of activity of a second effector protein; and c. comparing the first signal and the second signal. [0291] Embodiment 55: The method of Embodiment 54, wherein assaying for at least one target nucleic acid comprising the genomic variant comprises: (i) contacting at least a first portion of the sample to a first composition comprising a first effector protein, a first guide nucleic acid, and a first reporter; and (ii) detecting the presence or absence of a target nucleic acid comprising the genomic variant by assaying for a first signal, or change in first signal, produced by trans cleavage of the first reporter by the first effector protein, wherein the trans cleavage is activated upon hybridization of the first guide nucleic acid to the target nucleic acid molecule comprising the genomic variant. [0292] Embodiment 56: The method of Embodiment 54 or 55, wherein assaying for at least one target nucleic acid not comprising the genomic variant comprises: (i) contacting at least a second portion of the sample to: a second composition comprising a second effector protein, a second guide nucleic acid, and a second reporter; and (ii) detecting the presence or absence of a target nucleic acid not comprising the genomic variant by assaying for a second signal, or change second in signal, produced by trans cleavage of the second reporter by the second effector protein, wherein the trans cleavage is activated upon hybridization of the second guide nucleic acid to the target nucleic acid molecule not comprising the genomic variant. [0293] Embodiment 57: The method of any one of Embodiments 54-56, wherein the genomic variant is an SNP. [0294] Embodiment 58: The method of Embodiment 57, comprising determining whether the organism is homozygous or heterozygous for the SNP. [0295] Embodiment 59: The method of Embodiment 58, wherein determining whether the organism is homozygous or heterozygous for the SNP comprises comparing the level of the first detectable signal to the level of the second detectable signal. [0296] Embodiment 60: The method of Embodiment 59, comprising identifying the organism as heterozygous for the SNP if the level of the first detectable signal is about equal to the level of the second detectable signal. [0297] Embodiment 61: The method of Embodiment 59, comprising identifying the organism as homozygous for the SNP if the level of the first detectable signal is higher than the level of the second detectable signal. [0298] Embodiment 62: The method of Embodiment 59, comprising identifying the organism as homozygous for a wild-type if the level of the second detectable signal is higher than the level of the first detectable signal. [0299] Embodiment 63: The method of any one of Embodiments 55-62, wherein the first reporter nucleic acid, the second reporter nucleic acid, or a combination thereof, comprise a fluorophore, a quencher, or a combination thereof. [0300] Embodiment 64: The method of any one of Embodiments 55-62, wherein the first reporter nucleic acid, the second reporter nucleic acid, or a combination thereof, comprise a fluorescence resonance energy transfer (FRET) pair. [0301] Embodiment 65: The method of any one of Embodiments 55-64, wherein the target nucleic acids are DNA. [0302] Embodiment 66: The method of any one of Embodiments 55-65, wherein the DNA is single or double stranded DNA. [0303] Embodiment 67: The method of any one of Embodiments 55-66, wherein the DNA is purified genomic DNA. [0304] Embodiment 68: The method of any one of Embodiments 65-66, wherein the DNA is pre-amplified DNA. [0305] Embodiment 69: The method of any one of Embodiments 55-64, wherein the target nucleic acids are RNA. [0306] Embodiment 70: The method of Embodiment 69, wherein the RNA is double stranded or single stranded RNA. [0307] Embodiment 71: The method of any one of Embodiments 69 or 70, wherein the RNA is purified genomic RNA. [0308] Embodiment 72: The method of any one of Embodiments 69 or 70, wherein the RNA is pre-amplified RNA. [0309] Embodiment 73: The method of any one of Embodiments 54-72, wherein the organism is selected from a group consisting of: unicellular organisms, multicellular organisms, pathogenic organisms, living organisms, or any combination thereof. [0310] Embodiment 74: The method of Embodiment 73, wherein the living organism is a human, an animal, a plant, a crop, or any combination thereof. [0311] Embodiment 75: The method of any one of Embodiments 54-74, wherein the assaying for the target nucleic acid comprising the SNP and the assaying for the target nucleic acid not comprising the SNP, are performed in a single reaction, in a single volume, or a combination thereof. [0312] Embodiment 76: The method of any one of Embodiments 54-75, wherein the first signal, the second signal, or a combination thereof, is detected at least at one point in time. [0313] Embodiment 77: The method of any one of Embodiments 54-76, wherein the reaction time for detecting the first signal, the second signal, or a combination thereof, is less than about 10 minutes. [0314] Embodiment 78: The method of any one of Embodiments 54-76, wherein the reaction time for detecting the first signal, the second signal, or a combination thereof, is less than about 15 minutes. [0315] Embodiment 79: The method of any one of Embodiments 54-76, wherein the reaction time for detecting the first signal, the second signal, or a combination thereof, is from about 10 minutes to about 30 minutes. [0316] Embodiment 80: The method of any one of Embodiments 54-62, comprising amplifying the target nucleic acid comprising the SNP, the target nucleic acid not comprising the SNP, or a combination thereof. [0317] Embodiment 81: The method of Embodiment 80, wherein the amplifying comprises: transcription mediated amplification (TMA), helicase dependent amplification (HDA), or circular helicase dependent amplification (cHDA), strand displacement amplification (SDA), recombinase polymerase amplification (RPA), loop mediated amplification (LAMP), exponential amplification reaction (EXPAR), rolling circle amplification (RCA), ligase chain reaction (LCR), simple method amplifying RNA targets (SMART), single primer isothermal amplification (SPIA), multiple displacement amplification (MDA), nucleic acid sequence based amplification (NASBA), hinge-initiated primer-dependent amplification of nucleic acids (HIP), nicking enzyme amplification reaction (NEAR), and improved multiple displacement amplification (IMDA), or any combination thereof. [0318] Embodiment 82: The method of Embodiment 80 or 81, wherein the amplification reaction time is from about 10 minutes to about 30 minutes. [0319] Embodiment 83: The method of Embodiment 80 or 81, wherein the amplification reaction time is less than about 20 minutes. [0320] Embodiment 84: The method of any one of Embodiments 54-83, wherein the assaying is carried out in vitro. [0321] Embodiment 85: The method of any one of Embodiments 54-84, wherein the first effector protein, the second effector protein, or a combination thereof, is a Type V or Type VI Cas effector protein. [0322] Embodiment 86: The method of Embodiment 85, wherein the type V Cas effector protein is a Cas12 protein. [0323] Embodiment 87: The method of Embodiment 86, wherein the Cas12 protein comprises a Cas12a polypeptide, a Cas12b polypeptide, a Cas12c polypeptide, a Cas12d polypeptide, a Cas12e polypeptide, a C2c4 polypeptide, a C2c8 polypeptide, a C2c5 polypeptide, a C2c10 polypeptide, or a C2c9 polypeptide. [0324] Embodiment 88: The method of any one of Embodiments 86-87, wherein the Cas12 protein is at least 80% identical to SEQ ID NO: 11. [0325] Embodiment 89: The method of any one of Embodiments 86-88, wherein the Cas12 protein is at least 95% identical to SEQ ID NO: 11. [0326] Embodiment 90: The method of any one of Embodiments 86-89, wherein the Cas12 protein is SEQ ID NO: 11. [0327] Embodiment 91: The method of Embodiment 85, wherein the type V Cas effector protein is a Cas14 protein. [0328] Embodiment 92: The method of Embodiment 91, wherein the Cas14 protein comprises a Cas14a polypeptide, a Cas14b polypeptide, a Cas14c polypeptide, a Cas14d polypeptide, a Cas14e polypeptide, a Cas14f polypeptide, a Cas14g polypeptide, a Cas14h polypeptide, a Cas14i polypeptide, a Cas14j polypeptide, or a Cas14k polypeptide. [0329] Embodiment 93: The method of Embodiment 85, wherein the type V Cas effector protein is a CasФ protein. [0330] Embodiment 94: The method of Embodiment 85, wherein the type VI Cas effector protein is a Cas13 protein. [0331] Embodiment 95: The method of Embodiment 94, wherein the Cas13 protein comprises a Cas13a polypeptide, a Cas13b polypeptide, a Cas13c polypeptide, a Cas13c polypeptide, a Cas13d polypeptide, or a Cas13e polypeptide. [0332] Embodiment 96: The method of any one of Embodiments 54-95, wherein the sample is suspended in a buffer composition. [0333] Embodiment 97: The method of any one of Embodiments 54-96, wherein the sample is suspended in a buffer composition with a pH of about 7 to about 9. [0334] Embodiment 98: The method of any one of Embodiments 54-97, wherein the sample is suspended in a buffer composition that enhances DNA detection. [0335] Embodiment 99: The method of any one of Embodiments 54-98, wherein the sample comprises at most 250 target nucleic acid copies per assay. [0336] Embodiment 100: The method of any one of Embodiments 54-99, wherein the SNP is associated with a disease. [0337] Embodiment 101: The method of Embodiment 100, wherein the disease a cancer, an inherited disorder, an ophthalmological disorder, or a combination thereof. [0338] Embodiment 102: The method of Embodiment 101, wherein the disease is cancer, an endocrinological disorder, an autoimmune disorder, or a metabolic disorder. [0339] Embodiment 103: The method of Embodiment 102, wherein the metabolic disorder is nonalcoholic fatty liver disease, alcoholic liver disease, liver disease, hepatitis, chronic hepatitis, hepatocellular carcinoma, diabetes, cirrhosis, steatosis, fibrosis, or obesity. [0340] Embodiment 104: The method of Embodiment 103, wherein the metabolic disorder is liver disease. [0341] Embodiment 105: The method of Embodiment 104, wherein the SNP is associated with a disease selected from a group consisting of: asthma, arrhythmia, blood pressure, biliary cirrhosis, bipolar affective disorder, colorectal cancer, Crohn’s Disease, dyslipidemia, eating disorder, esophageal adenocarcinoma, hyperbilirubinemia, idiopathic arthritis, idiopathic PD and FTD, knee and hip osteoarthritis, lung cancer, myocardial infraction, migraine, obesity, ossification, oxalate stone, POAG, rheumatoid arthritis, systemic sclerosis, severe sepsis, Type II diabetes, ulcerative colitis, urinary bladder cancer, and autism. [0342] Embodiment 106: The method of any one of Embodiments 54-105, wherein the target nucleic acid comprising the SNP, the target nucleic acid not comprising the SNP, or a combination thereof, is, or is encoded by, a gene selected from a group consisting of: EDN1, NOS1, KCN1, TAF1, MBL, HRT 3A, Cyclin D1, UGT1A1 UDP, MIF, SNCA, LRRK2, MMP1, PAI, PAI1, Npps, CDH, CDH1, POAG, TNF, TNF-α, MDR1, TSP, PCS, PNPLA3, IR, INSR, CNP, LPL, MCR, MC1R, TMEM, C9ORF72, MAPT, GRN, COL, p53, MYOC, FBN1, STX1A, CCN, CCND1 cyclin D1, a fragment thereof, or any combination thereof. [0343] Embodiment 107: The method of any one of Embodiments 54-106, wherein the target nucleic acid comprising the SNP, the target nucleic acid not comprising the SNP, or a combination thereof, is, or is encoded by, a PNPLA3 gene, or a fragment thereof. [0344] Embodiment 108: The method of Embodiment 107, wherein the target nucleic acid comprising the SNP is a PNPLA3 gene comprising a substitution of a C with a G at nucleotide position 444 of SEQ ID NO: 384, or a fragment thereof. [0345] Embodiment 109: The method of Embodiment 108, wherein the PNPLA3 gene encodes a PNPLA3 protein comprising an I to M substitution at amino acid position of 148 of SEQ ID NO: 385. [0346] Embodiment 110: The method of any one of Embodiments 54-109, wherein the target nucleic acid not comprising the SNP is a wild-type PNPLA3 gene, or a fragment thereof. [0347] Embodiment 111: The method of any one of Embodiments 54-110, wherein the target nucleic acid not comprising the SNP is a PNPLA3 gene comprising a substitution at nucleotide position 443 of a wild-type PNPLA3 gene, or a fragment thereof. [0348] Embodiment 112: The method of Embodiment 97, wherein the Cas12 protein associates with a gRNA comprising a nucleotide sequence that is at least 75% identical to any one of SEQ ID NOs: 209-366. [0349] Embodiment 113: The method of Embodiment 97, wherein the Cas12 protein associates with a gRNA comprising a nucleotide sequence that is at least 95% identical to any one of SEQ ID NOs: 209-366. [0350] Embodiment 114: The method of Embodiment 97, wherein the Cas12 protein associates with a gRNA comprising a nucleotide sequence that is at least 100% identical to any one of SEQ ID NOs: 209-366. [0351] Embodiment 115: The method of any one of Embodiments 56-62, wherein the first effector protein and the second effector protein are Cas12 proteins comprising a sequence with at least 80%, 95%, or 100% identity to SEQ ID NO: 11. EXAMPLES [0352] The following examples are illustrative and non-limiting to the scope of the compositions, and methods described herein. EXAMPLE 1: PNPLA3 DETECTR Assay [0353] A DETECTR assay is used to distinguish the presence or absence of single nucleotide polymorphisms in purified genomic DNA comprising the PNPLA3 (patatin-like phospholipase domain-containing protein 3) gene. The PNPLA3 gene contains two SNP sites separated by only two nucleotide bases. A first single nucleotide mutation (rs738409) leads to a I148M amino acid substitution associated with an increased risk of nonalcoholic fatty liver disease. A second single nucleotide mutation (rs738408) codes a silent mutation with a 70% linkage to the at-risk allele. The DETECTR assay comprised amplifying genomic DNA in an amplification reaction and then contacting it with a composition comprising a Cas12 effector protein and guide RNA complex in a subsequent detection reaction. FIG.1 illustrates an assay workflow for detecting the at-risk alleles of a target gene in about 30 minutes using a Cas12 effector protein and either a guide which targets the wild type allele (“WT PNPLA3”) or the at- risk allele (“I148M PNPLA3”). As shown, purified genomic DNA, undergoes pre-amplification for about 15 minutes followed by detection with either (1) the Cas12 effector protein complexed with the guide nucleic acid targeting the wild type allele or (2) the Cas12 effector protein complexed with the guide nucleic acid targeting the at-risk allele, in a detection reaction having a 15 minute reaction time. EXAMPLE 2: PNPLA3 DETECTR Assay [0354] A DETECTR assay was used to distinguish the presence or absence of single nucleotide polymorphisms in purified genomic DNA comprising the PNPLA3 (patatin-like phospholipase domain-containing protein 3) gene. The DETECTR assay comprised amplifying genomic DNA in an amplification reaction and then contacting it with a composition comprising an effector protein (e.g., SEQ ID NO: 11) and guide RNA complex in a detection reaction. Table 4 details the guide RNAs designed to be compatible with the effector protein (a Cas12 protein, SEQ ID NO: 11) and to hybridize to certain PNPLA3 SNPs. Specifically, the guide nucleic acids were designed to distinguish (i) the at-risk allele (rs738409) from (ii) the non-risk allele (rs738408) and the wild type allele. FIG.1 illustrates an exemplary experimental workflow for purified genomic DNA. Genomic DNA was pre-amplified for 20 minutes, prior to being subject to the Cas12 detection reaction. The amplified sample was split into fractions and contacted with either (1) the Cas12 effector protein complexed with the guide nucleic acid targeting the wild type allele / non-risk allele; or (2) the Cas12 effector protein complexed with the guide nucleic acid targeting the at-risk allele. The Cas12 detection reaction was performed for 15 minutes, allowing for a total reaction time of 36 minutes. FIG.3 is a multi-panel diagram illustrating the results of the DETECTR reactions performed using lysed crude buccal swab samples generated in four different buccal swab lysis buffer compositions. The Y axis of the diagram notes the buccal swab lysis buffer composition used during sample prep (“Buffer 1,” “Buffer 2,” “Buffer 3,” and “Buffer 4”), and whether the detection reagents included a complex comprising a wild- type guide or risk-allele complementary guide. The X axis denotes the genotype of each sample tested, classifying each sample as having either (1) two wild-type alleles (“WT/WT”); (2) a wild- type allele and a non-risk allele (“WT/408”); (3) a wild-type allele and a risk allele (“WT/409”); (4) a non-risk allele and a risk allele (“408/409”); or (5) two risk alleles, including samples comprising both risk and non-risk alleles (“409/409,” “409 / 409+408,” “409+408 / 409 +408”). The darker blue panels indicate a higher level of fluorescence produced by the detection reaction, with the lighter yellow panels indicating a lower level of fluorescence produced by the detection reaction. As illustrated in FIG.3, the effector protein complexes were able to distinguish between target nucleic acids comprising the at-risk allele and those not containing the at-risk allele in the same sample. Under the conditions tested, Buffer Composition 3 (1x phosphate buffered saline (PBS) and 1M NaOH, having a pH of 7.4) performed the strongest and enabled the different effector protein complexes (comprising wild-type versus at-risk guides) to produce distinct levels of fluorescence for at-risk alleles and non-risk alleles from the same lysed crude sample. FIG.4 includes graphs measuring the results of the amplification assays performed on 2.5 uL of the crude samples in three different reaction conditions designed to determine if the reaction could be improved by removing glycerol and increasing the primer concentration, with different reagent mixtures for a 30 minute amplification reaction time at 63 ^C. The “original enzyme mix” included Bst 2.0 DNA polymerase in glycerol while the “new enzyme mix” included Bst 2.0 from a glycerol-free stock. “Condition 1” included a 1x concentration of LAMP primers, “Condition 2” included a 2x concentration of LAMP primers, and “Condition 3” included a 4x concentration of LAMP primers. FIG.5A shows a graph measuring the amplification assay results, measured in raw fluorescence, when performed for 15 minutes, and FIG.5B shows the results of the detection assay performed on the amplified product. [0355] The primer, reporter, and gRNA sequences used in this assay are provided in Tables 6-8 below. Table 6: gRNA Sequences

Table 7: Reporter Sequences

Table 8: Primer Sequences

EXAMPLE 3: PNPLA DETECTR Assay Genotyping [0356] A DETECTR assay was used to distinguish the presence or absence of single nucleotide polymorphisms in purified genomic DNA, obtained from a crude sample, comprising the PNPLA3 (patatin-like phospholipase domain-containing protein 3) gene. The DETECTR assay comprised genomic DNA from a crude sample in an amplification reaction and then contacting it with a composition comprising an effector protein (SEQ ID NO: 11) and guide RNA complex in a detection reaction. Table 4 details the guide RNAs designed to be compatible with the effector protein (a Cas12 protein, SEQ ID NO: 11) and to hybridize to the PNPLA3 SNPs. Specifically, the guide nucleic acids were designed to distinguish (i) the at-risk allele (rs738409) from (ii) the non-risk allele (rs738408) and the wild type allele. FIG.2 illustrates the experimental workflow. A crude sample was formulated in a lysis buffer and pre-amplified for 20 minutes, prior to being subject to the Cas12 detection reaction. The amplified sample was split into fractions and contacted with either (1) the Cas12 effector protein complexed with the guide nucleic acid targeting the wild type allele / non-risk allele; or (2) the Cas12 effector protein complexed with the guide nucleic acid targeting the at-risk allele. The Cas12 detection reaction was performed for 15 minutes, allowing for a total reaction time of 36 minutes. [0357] Samples containing synthetic control nucleic acids were assayed to determine a baseline fluorescence for each PNPLA3 genotype. The DETECTR assays detect a wild type allele, at-risk allele, or non-risk allele of PNPLA3. Fluorescence data was used to genotype the samples as homozygous or heterozygous for the PNPLA3 SNPs. FIG.5 shows the results of a DETECTR assay measuring synthetic control samples for different genetic combinations of PNPLA3 alleles, as measured in raw florescence (au). FIG.5A shows samples target amplified with loop-mediated isothermal amplification (LAMP), as compared to DETECTR data in FIG. 5B. Samples containing wild type synthetic control DNA (“wild-type control”), both wild type and at-risk allele synthetic control DNA (“het control”), at-risk allele synthetic control DNA (“mutant control”), or no target (“NTC”) were detected using gRNA directed to either the wild type sequence (“WT gRNA”) or the at-risk allele (“Mutant gRNA”). The resulting data was analyzed to determine threshold fluorescence ratios differentiate wild type, mutant, and heterozygous phenotypes. As seen in FIG.6, raw fluorescence data was used to calculate fluorescence intensity ratios to distinguish between wild type, heterozygous, and at-risk sequences. Together, these results show that DETECTR can be used to differentiate samples that are homozygous or heterozygous for single nucleotide polymorphisms. EXAMPLE 4: Detection of At-Risk PNPLA3 Alleles in Clinical Samples [0358] Three fragments of ten clinical samples were pre-amplified and assayed for detection of a wild type allele, at-risk allele, or non-risk allele of PNPLA3 with DETECTR assay. [0359] A protocol for genotyping the human gene PNPLA3 for the I148M (rs738409) mutation using a DETECTR assay was used. Substantially the same DETECTR protocol was used in Examples 2 and 3 disclosed herein (e.g., apart from certain experiments in which varying buffer compositions were used). The protocol required the following materials: ● Plate reader capable of reading AF594 (excitation: 590 nm, emission: 617 nm) ● 384-well assay plate (suggested: Corning 3821 or Bio-Rad HSP3866) ● 96-well PCR plate or PCR strip tubes ● qPCR machine or heat block capable of reaching 63°C ● 1.5 mL microcentrifuge tubes ● 15 mL falcon tube ● Buccal Swab Extraction Buffer (Mammoth; 1x PBS, 1M NaOH, pH 7.4) ● Nuclease-Free Water ● 10X Isothermal Amplification Buffer (NEB, B0537S) ● 100 mM MgsO4 (NEB, B1003S) ● 10 mM dNTP (NEB, N0447L) ● Bst 2.0 Polymerase, glycerol-free (NEB) ● Control gene fragments: ○ WT-control: 10,000 copies/µL WT ○ Het-control: 5,000 copies/µL WT + 5,000 copies/µL mutant ○ Mut-control: 10,000 copies/µL mutant ● 50 µM SYTO9 (optional) ● 5X MBuffer 3 (Mammoth; 20 mM HEPES, pH 7.52 mM KOAc 5 mM MgOAc 5% Glycerol 0.016% Triton-X 100) ● 5 µM Cas 12 Ortholog (Mammoth, SEQ ID NO: 11) ● 20 µM crRNAs ○ WT PNPLA3 ■ R1287 (WT-1) ■ R1434 (WT-2) ○ I148M PNPLA3 ■ R1327 (mut-1) ■ R1435 (mut-2) ● 100 µM reporter substrate (rep033) ● 10X primer mix (F3, B3, FIP, BIP, LF, LB) in nuclease-free water ○ Primers should be HPLC purified (IDT) ○ 10X stock concentration for primers ■ M1543 (F3) - 2 µM ■ M1544 (B3) - 2 µM ■ M1545 (FIP) - 16 µM ■ M1546 (BIP) - 16 µM ■ M1547 (LF) - 8 µM [0360] First, the crude samples were extracted from buccal swabs.2 mL of Buccal Swab Extract Buffer was placed in a 15 mL falcon tube. The dry buccal swab was removed from the collection tube and placed into a buffer. While submerged in the buffer, the swab was scraped and pressed along the side of the tube to maximize elution of the material. The swab was then discarded and the sample was allowed to sit for 1 minute at room temperature. Next, the target DNA was pre-amplified, using a LAMP master mix comprising the below components:

[0361] After adding primers, the reaction mix was placed on an ice / cold-block.22.5 µL of the master mix was then aliquoted into a 96-well plate (PCR tubes may also be used).2.5 µL of target DNA (crude extraction or controls) was then added to each well. Then the plate was sealed with PCR film and spun down. The reaction then was run on a heat block under the following parameters: i. Time of run: 20 minutes ii. Temperature: 63°C iii. If using SYTO9, monitor amplification every 30 seconds in FAM channel [0362] After, the LAMP reaction was removed and placed on ice until the DETECTR reaction was ready to begin. To run the DETECTR reaction, first the following Cas12 complexing reaction master-mixes were prepared: i. WT PNPLA3 complexing reaction

ii. I148M PNPLA3 complexing reaction

[0363] The complexing mixes were then incubated at 37C for 30 minutes.100 µM reporter substrate rep033 was then added to the final concentration of 400 nM per 5 µL complexing reaction (0.02 µL per reaction). In a 384-well black assay plate, 14 µL of 1X MBuffer 3 were then distributed into wells on ice. After 5 µL of complexing reaction were added to appropriate wells. In a post-amp hood, 2 µL of LAMP product was added to appropriate wells. While the plate was on ice, it was sealed with optically clear film and spun down for 30 sec at 2000 rcf. It was then Read on a fluorescent plate reader monitoring continuously for a run time of 15 minutes. The interval between reads was 1 min, the temperature was 37°C, the fluorophore used was AF594 (590 / 617). End-point fluorescence was analyzed at 15 minutes after starting the DETECTR reaction. Valid results were expected to show maximal signal from WT PNPLA3 DETECTR in WT control reactions and maximal signal from I148M PNPLA3 DETECTR in mutant control reactions. [0364] End-point fluorescence was used to calculate the following for each replicate / reaction, where X_wt is the signal from the WT PNPLA3 DETECTR reaction, and X_mut is the signal from the I148M PNPLA3 DETECTR reaction:

The values of S > 0.4 are considered WT, the values of 0.4 > S > -0.4 are considered heterozygous, and the values of S < 0.4 are considered mutant. Threshold values may depend on the specific experimental set up. [0365] DETECTR fluorescence data was used to genotype the clinical samples as homozygous or heterozygous for the PNPLA3 SNPs, as compared to DETECTR fluorescence data for synthetic control samples for different genetic combinations of PNPLA3 alleles. Florescence (au) data for synthetic control samples for different genetic combinations of PNPLA3 alleles was used to determine a baseline fluorescence ratio for each PNPLA3 genotype. FIG. 8 depicts graphs showing the results of the PNPLA3 DETECTR reaction, as measured in raw fluorescence, performed on ten different blinded clinical samples. FIG. 8A shows the ten samples target amplified with loop-mediated isothermal amplification (LAMP), as measured in raw florescence. FIG. 8B shows DETECTR assay measuring the samples for different genetic combinations of PNPLA3 alleles, as measured in raw florescence. FIG. 9 depicts a graph showing a re-run of the PNPLA3 DETECTR reaction on select clinical samples, from the group of 10 clinical samples referenced in FIGS. 7 and 8. FIG. 10 depicts gel electrophoresis for DNAs extracted from samples 127-1453, 127-1452, and 127-1447, referenced in FIGS. 7-9, and amplified by PNPLA3 specific PCR. 127-1453 failed to amplify by PCR, which suggests that there might have been very little genetic material on the sample swab. FIG. 11 depicts a graph showing a re-run of the PNPLA3 DETECTR reaction on select clinical samples, from the group of 10 clinical samples referenced in FIGS. 7 and 8 with a 30 minute detection reaction time. FIG. 12 depicts a graph showing a re-run of the PNPLA3 DETECTR reaction on select clinical samples, from the group of 10 clinical samples referenced in FIGS. 7 and 8 to examiner variability among multiple replicate runs. FIG.13 shows the results of a DETECTR assay fluorescence ratio for the ten clinical samples. The DETECTR assay fluorescence ratio data was used to determine wild type, mutant, and heterozygous phenotypes as compared to threshold fluorescence ratios. As shown in FIG. 7, DETECTR fluorescence data from three repeat assays of ten clinical samples was used to genotype the clinical samples as homozygous or heterozygous for the PNPLA3 SNPs. EXAMPLE 5: Pooled gRNAs to Distinguish Two SNPs in PNPLA3 [0366] This example describes pooled gRNAs to distinguish two single nucleotide polymorphisms in PNPLA3. Guide RNAs identified in Table 4 that are specific for a single PNPLA3 allele are pooled for detection of at-risk alleles. In a first assay, gRNAs are tested individually to confirm specificity of each gRNA for the targeted SNP combination. Samples are detected using a Cas12 programmable nuclease (SEQ ID NO: 11). A negative control lacking a target nucleic acid is also run to confirm that the system is performing properly. [0367] Guide RNAs directed to the WT allele and the rs738408 allele are then pooled for detection of the WT allele and the non-risk allele in the absence of the at-risk allele. Guide RNAs directed to the rs738409 allele and the rs738409+408 allele are pooled for the detection of the at- risk allele independent of the presence or absence of the non-risk allele. Pools of gRNA are designed to detect the wild type or non-risk alleles or at-risk allele independent of the presence or absence of the non-risk allele. Samples are detected using a Cas12 programmable nuclease (SEQ ID NO: 11). A negative control lacking a target nucleic acid is also run to confirm that the system is performing properly. [0368] While preferred embodiments of the present disclosure 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 disclosure. It should be understood that various alternatives to the embodiments of the disclosure described herein may be employed in practicing the disclosure. It is intended that the following claims define the scope of the disclosure and that methods and structures within the scope of these claims and their equivalents be covered thereby.

Claims

CLAIMS 1. A method for determining a variant genotype in an organism, comprising: a. assaying for at least one target nucleic acid comprising a genomic variant in a sample by assaying for a first signal indicative of activity of a first effector protein; b. assaying for at least one target nucleic acid not comprising the genomic variant in the sample by assaying for a second signal indicative of activity of a second effector protein; and c. comparing the first signal and the second signal.

2. The method of claim 1, wherein assaying for at least one target nucleic acid comprising the genomic variant comprises: (i) contacting at least a first portion of the sample to a first composition comprising a first effector protein, a first guide nucleic acid, and a first reporter; and (ii) detecting the presence or absence of a target nucleic acid comprising the genomic variant by assaying for a first signal, or change in first signal, produced by trans cleavage of the first reporter by the first effector protein, wherein the trans cleavage is activated upon hybridization of the first guide nucleic acid to the target nucleic acid molecule comprising the genomic variant.

3. The method of claim 2, wherein assaying for at least one target nucleic acid not comprising the genomic variant comprises: (i) contacting at least a second portion of the sample to: a second composition comprising a second effector protein, a second guide nucleic acid, and a second reporter; and (ii) detecting the presence or absence of a target nucleic acid not comprising the genomic variant by assaying for a second signal, or change second in signal, produced by trans cleavage of the second reporter by the second effector protein, wherein the trans cleavage is activated upon hybridization of the second guide nucleic acid to the target nucleic acid molecule not comprising the genomic variant.

4. The method of claim 3, wherein the first effector protein and the second effector protein are Cas12 proteins comprising a sequence with at least 80%, 95%, or 100% identity to SEQ ID NO: 11.

5. The method of claim 1, wherein the genomic variant is a SNP.

6. The method of claim 5, comprising determining whether the organism is homozygous or heterozygous for the SNP.

7. The method of claim 6, wherein determining whether the organism is homozygous or heterozygous for the SNP comprises comparing the level of the first detectable signal to the level of the second detectable signal.

8. The method of claim 7, further comprising: (a) identifying the organism as heterozygous for the SNP if the level of the first detectable signal is about equal to the level of the second detectable signal; (b) identifying the organism as homozygous for the SNP if the level of the first detectable signal is higher than the level of the second detectable signal; or (c) identifying the organism as homozygous for a wild-type if the level of the second detectable signal is higher than the level of the first detectable signal.

9. The method of claim 8, wherein the first effector protein and the second effector protein are Cas12 proteins comprising a sequence with at least 80%, 95%, or 100% identity to SEQ ID NO: 11.

10. The method of claim 3, wherein (a) the first reporter nucleic acid, the second reporter nucleic acid, or a combination thereof, comprise a fluorophore, a quencher, or a combination thereof; or (b) the first reporter nucleic acid, the second reporter nucleic acid, or a combination thereof, comprise a fluorescence resonance energy transfer (FRET) pair.

11. The method of claim 2, wherein the target nucleic acids are DNA; optionally wherein the DNA is single-stranded DNA, double stranded DNA, purified genomic DNA, or pre- amplified DNA.

12. The method of claim 2, wherein the target nucleic acids are RNA; optionally wherein the RNA is double-stranded RNA, single stranded RNA, purified genomic RNA, or pre- amplified RNA.

13. The method of claim 1, wherein the organism is (a) selected from a group consisting of unicellular organisms, multicellular organisms, pathogenic organisms, living organisms, or any combination thereof; or (b) a human, an animal, a plant, or a crop.

14. The method of claim 1, wherein the assaying for the target nucleic acid comprising the SNP and the assaying for the target nucleic acid not comprising the SNP, are performed in a single reaction, in a single volume, or a combination thereof.

15. The method of claim 1, wherein the reaction time for detecting the first signal, the second signal, or a combination thereof, is less than 15 minutes, less than 10 minutes, or from about 10 minutes to about 30 minutes.

16. The method of claim 1, further comprising amplifying the target nucleic acid comprising the SNP, the target nucleic acid not comprising the SNP, or a combination thereof.

17. The method of claim 16, wherein the amplifying comprises: transcription mediated amplification (TMA), helicase dependent amplification (HDA), or circular helicase dependent amplification (cHDA), strand displacement amplification (SDA), recombinase polymerase amplification (RPA), loop mediated amplification (LAMP), exponential amplification reaction (EXPAR), rolling circle amplification (RCA), ligase chain reaction (LCR), simple method amplifying RNA targets (SMART), single primer isothermal amplification (SPIA), multiple displacement amplification (MDA), nucleic acid sequence based amplification (NASBA), hinge-initiated primer-dependent amplification of nucleic acids (HIP), nicking enzyme amplification reaction (NEAR), and improved multiple displacement amplification (IMDA), or any combination thereof.

18. The method of claim 16, wherein the amplification reaction time is less than 20 minutes, or from about 10 minutes to about 30 minutes.

19. The method of claim 1, wherein the assaying is carried out in vitro.

20. The method of claim 1, wherein the first effector protein, the second effector protein, or a combination thereof, is a Type V or Type VI Cas effector protein.

21. The method of claim 20, wherein the type V Cas effector protein is a Cas12 protein; optionally wherein the Cas12 protein comprises a Cas12a polypeptide, a Cas12b polypeptide, a Cas12c polypeptide, a Cas12d polypeptide, a Cas12e polypeptide, a C2c4 polypeptide, a C2c8 polypeptide, a C2c5 polypeptide, a C2c10 polypeptide, or a C2c9 polypeptide.

22. The method of claim 21, wherein the Cas12 protein comprises a sequence with at least 80%, 95%, or 100% identity to SEQ ID NO: 11.

23. The method of claim 20, wherein the type V Cas effector protein is a Cas14 protein; optionally wherein the Cas14 protein comprises a Cas14a polypeptide, a Cas14b polypeptide, a Cas14c polypeptide, a Cas14d polypeptide, a Cas14e polypeptide, a Cas14f polypeptide, a Cas14g polypeptide, a Cas14h polypeptide, a Cas14i polypeptide, a Cas14j polypeptide, or a Cas14k polypeptide.

24. The method of claim 20, wherein the type V Cas effector protein is a CasФ protein.

25. The method of claim 20, wherein the type VI Cas effector protein is a Cas13 protein; optionally wherein the Cas13 protein comprises a Cas13a polypeptide, a Cas13b polypeptide, a Cas13c polypeptide, a Cas13c polypeptide, a Cas13d polypeptide, or a Cas13e polypeptide.

26. The method of claim 1, wherein the sample is suspended in a buffer composition; optionally wherein the buffer composition enhances DNA detection.

27. The method of claim 1, wherein the sample is suspended in a buffer composition with a pH of about 7 to about 9.

28. The method of claim 1, wherein the sample comprises at most 250 target nucleic acid copies per assay.

29. The method of claim 1, wherein the SNP is associated with a disease.

30. The method of claim 29, wherein: (a) the disease is a cancer, an inherited disorder, an ophthalmological disorder, an endocrinological disorder, an autoimmune disorder, or a metabolic disorder or a combination thereof; (b) the disease is a metabolic disorder, wherein the metabolic disorder is nonalcoholic fatty liver disease, alcoholic liver disease, liver disease, hepatitis, chronic hepatitis, hepatocellular carcinoma, diabetes, cirrhosis, steatosis, fibrosis, or obesity; or (c) the disease is selected from a group consisting of: asthma, arrhythmia, blood pressure, biliary cirrhosis, bipolar affective disorder, colorectal cancer, Crohn’s Disease, dyslipidemia, eating disorder, esophageal adenocarcinoma, hyperbilirubinemia, idiopathic arthritis, idiopathic PD and FTD, knee and hip osteoarthritis, lung cancer, myocardial infraction, migraine, obesity, ossification, oxalate stone, POAG, rheumatoid arthritis, systemic sclerosis, severe sepsis, Type II diabetes, ulcerative colitis, urinary bladder cancer, and autism.

31. The method of claim 1, wherein the target nucleic acid comprising the SNP, the target nucleic acid not comprising the SNP, or a combination thereof, is, or is encoded by, a gene selected from a group consisting of: EDN1, NOS1, KCN1, TAF1, MBL, HRT 3A, Cyclin D1, UGT1A1 UDP, MIF, SNCA, LRRK2, MMP1, PAI, PAI1, Npps, CDH, CDH1, POAG, TNF, TNF-α, MDR1, TSP, PCS, PNPLA3, IR, INSR, CNP, LPL, MCR, MC1R, TMEM, C9ORF72, MAPT, GRN, COL, p53, MYOC, FBN1, STX1A, CCN, CCND1 cyclin D1, a fragment thereof, or any combination thereof.

32. The method of claim 1, wherein the target nucleic acid comprising the SNP, the target nucleic acid not comprising the SNP, or a combination thereof, is, or is encoded by, a PNPLA3 gene, or a fragment thereof.

33. The method of claim 32, wherein (a) the PNPLA3 gene comprises a substitution of a C with a G at nucleotide position 444 of SEQ ID NO: 384, and/or (b) the PNPLA3 gene encodes a PNPLA3 protein comprising an I to M substitution at amino acid position of 148 of SEQ ID NO: 385.

34. The method of claim 1, wherein the target nucleic acid not comprising the SNP is (a) a wild- type PNPLA3 gene, or a fragment thereof; or (b) a PNPLA3 gene comprising a substitution at nucleotide position 443 of SEQ ID NO: 384.

35. The method of claim 27, wherein the Cas12 protein associates with a gRNA comprising a nucleotide sequence that is at least 75%, 95%, or 100% identical to any one of SEQ ID NOs: 209-366.

36. A method of assaying for a target nucleic acid comprising a nucleotide variant at a position of interest, the method comprising: (a) contacting a sample to: (i) a composition comprising an effector protein and a guide nucleic acid; and (ii) a reporter, and (b) detecting a presence or absence of a target nucleic acid comprising the nucleotide variant in the sample by assaying for a signal indicative of cleavage of the reporter by the effector protein; wherein the detecting comprises comparing the signal to a control signal produced by contacting the composition and reporter to a control nucleic acid molecule not comprising the nucleotide variant, but that is otherwise identical to the target nucleic acid, at least apart from a variation of less than twenty nucleotides.

37. The method of claim 36, wherein assaying for a signal produced by the effector protein comprises assaying for a signal, or change in signal, produced by trans cleavage of the reporter by the effector protein, wherein the trans cleavage is activated upon hybridization of the guide nucleic acid to the target nucleic acid molecule comprising the nucleotide variant 38. The method of claim 36, wherein the control nucleic acid molecule is otherwise identical to the target nucleic acid molecule, apart from a variation of less than four nucleotides or less than two nucleotides. 39. The method of claim 36, wherein the control nucleic acid molecule is otherwise identical to the target nucleic acid molecule. 40. The method of claim 36, wherein the nucleotide variant is: (a) a point mutation in the target nucleic acid molecule, relative to an otherwise identical target nucleic acid molecule; (b) a non-synonymous mutation; (c) a synonymous mutation; (d) a missense mutation, a nonsense mutation, or a non-stop mutation; or (e) a single nucleotide polymorphism (SNP) 41. The method of claim 36, wherein the nucleotide variant is associated with a disease. 42. The method of claim 41, wherein: (a) the disease is a cancer, an inherited disorder, an ophthalmological disorder, an endocrinological disorder, an autoimmune disorder, a metabolic disorder, or a combination thereof; (b) the disease is a metabolic disorder, wherein the metabolic disorder is nonalcoholic fatty liver disease, alcoholic liver disease, liver disease, hepatitis, chronic hepatitis, hepatocellular carcinoma, diabetes, cirrhosis, steatosis, fibrosis, obesity, or a combination thereof; or (c) the disease is selected from a group consisting of: asthma, arrhythmia, blood pressure, biliary cirrhosis, bipolar affective disorder, colorectal cancer, Crohn’s Disease, dyslipidemia, eating disorder, esophageal adenocarcinoma, hyperbilirubinemia, idiopathic arthritis, idiopathic PD and FTD, knee and hip osteoarthritis, lung cancer, myocardial infraction, migraine, obesity, ossification, oxalate stone, POAG, rheumatoid arthritis, systemic sclerosis, severe sepsis, Type II diabetes, ulcerative colitis, urinary bladder cancer, and autism. 43. The method of claim 36, wherein the target nucleic acid is, or is encoded by, a gene selected from a group consisting of: EDN1, NOS1, KCN1, TAF1, MBL, HRT 3A, Cyclin D1, UGT1A1 UDP, MIF, SNCA, LRRK2, MMP1, PAI, PAI1, Npps, CDH, CDH1, POAG, TNF, TNF-α, MDR1, TSP, PCS, PNPLA3, IR, INSR, CNP, LPL, MCR, MC1R, TMEM, C9ORF72, MAPT, GRN, COL, p53, MYOC, FBN1, STX1A, CCN, CCND1 cyclin D1, a fragment thereof, or any combination thereof. 44. The method of claim 36, wherein the target nucleic acid is, or is encoded by, a PNPLA3 gene or a fragment thereof. 45. The method of claim 44, wherein (a) the PNPLA3 gene comprises a substitution of a C with a G at nucleotide position 444 of SEQ ID NO: 384, and/or (b) the PNPLA3 gene encodes a PNPLA3 protein comprising an I to M substitution at amino acid position of 148 of SEQ ID NO: 385. 46. The method claim 36, wherein the nucleotide variant is an SNP, a marker of a disease, or a combination thereof. 47. The method of claim 46, further comprising determining whether an organism from which the sample is derived is homozygous or heterozygous for the nucleotide variant. 48. The method of claim 36, wherein the effector protein is a Type V or Type VI Cas effector protein. 49. The method of claim 48, wherein the type V Cas effector protein is a Cas12 protein; optionally wherein the Cas12 protein comprises a Cas12a polypeptide, a Cas12b polypeptide, a Cas12c polypeptide, a Cas12d polypeptide, a Cas12e polypeptide, a C2c4 polypeptide, a C2c8 polypeptide, a C2c5 polypeptide, a C2c10 polypeptide, or a C2c9 polypeptide. 50. The method of claim 49, wherein the Cas12 protein comprises a sequence with at least 80%, 95%, or 100% identity to SEQ ID NO: 11. 51. The method of claim 48, wherein the type V Cas effector protein is a Cas14 protein; optionally wherein the Cas14 protein comprises a Cas14a polypeptide, a Cas14b polypeptide, a Cas14c polypeptide, a Cas14d polypeptide, a Cas14e polypeptide, a Cas14f polypeptide, a Cas14g polypeptide, a Cas14h polypeptide, a Cas14i polypeptide, a Cas14j polypeptide, or a Cas14k polypeptide. 52. The method of claim 48, wherein the type V Cas effector protein is a CasФ protein. 53. The method of claim 48, wherein the type VI Cas effector protein is a Cas13 protein; optionally wherein the Cas13 protein comprises a Cas13a polypeptide, a Cas13b polypeptide, a Cas13c polypeptide, a Cas13c polypeptide, a Cas13d polypeptide, or a Cas13e polypeptide. 54. The method of claim 36, wherein (a) the reporter comprises a fluorophore, a quencher, or a combination thereof; or (b) the reporter comprises a fluorescence resonance energy transfer (FRET) pair. 55. The method of claim 36, wherein the target nucleic acid is DNA; optionally wherein the DNA is single-stranded DNA, double stranded DNA, purified genomic DNA, or pre- amplified DNA. 56. The method of claim 36, wherein the target nucleic acid is RNA; optionally wherein the RNA is double-stranded RNA, single stranded RNA, purified genomic RNA, or pre- amplified RNA. 57. The method of claim 36, wherein the sample is suspended in a buffer composition; optionally wherein the buffer composition enhances DNA detection. 58. The method of claim 36, wherein the sample is suspended in a buffer composition with a pH of about 7 to about 9. 59. The method of claim 36, wherein the sample comprises at most 250 target nucleic acid copies per assay. 60. The method of claim 36, wherein the sample is derived from (a) an organism selected from the group consisting of unicellular organisms, multicellular organisms, pathogenic organisms, living organisms, or any combination thereof; or (b) a human, an animal, a plant, a crop, or any combination thereof. 61. The method of claim 58, wherein the Cas12 protein associates with a gRNA comprising a nucleotide sequence that is at least 75%, 95%, or 100% identical to any one of SEQ ID NOs: 209-366.