Scope & Usage

Scope

The module SMAP effect-prediction is designed to provide biological interpretation of the haplotype call tables created by SMAP haplotype-window.

It’s main functions are to:

Filter for haplotypes with edits in a defined region of interest (ROI; e.g. surrounding the PAM site for CRISPR/Cas experiments) to eliminate noise from the genotype table.

Substitute the segment of the original reference gene sequence by the observed haplotype, keeping track of all relevant coordinates of intron-exon borders, translational start and stop codons, and the open reading frame (ORF), and predict the resulting (mutated) protein sequence.

Compare the novel predicted protein sequence to the original reference protein and estimate the fraction of the protein length that is still encoded by the novel (mutated) allele.

Use a threshold for the %protein length required for (partial) loss of function, and classify all haplotypes by effect class (no/minimal effect, intermediate effect, loss-of-function).

Aggregate all observed haplotypes and sum their relative frequencies per effect class.

Finally, discretize the genotype calls as homozygous or heterozygous for reference versus loss of function at a user defined minimal effect level.

Plot summary statistics of editing “fingerprints” across the data set to allow the user to optimize parameter setting accoring to their experimental data.

Within the SMAP package, the modules SMAP target-selection, SMAP design, SMAP haplotype-window and SMAP effect-prediction are designed to provide a seamless workflow from target selection (e.g. candidate genes), integrated primer and gRNA design, multiplex resequencing of target loci across large plant collections, followed by identification of all observed haplotypes (naturally occuring or CRISPR-induced sequence variants), the prediction of functional effects of sequence variants at the protein level to identify (partial) loss-of-function (LOF) alleles, and finally aggregate and discretize genotype calls in an integrated genotype table with the homozygous/heterozygous presence of LOF alleles per locus per sample. The overarching goal of this entire workflow is to identify carriers of LOF alleles for functional analysis, or for genotype-phenotype associations.

Specifically, the underlying concepts of SMAP effect-prediction exploit:

Modularity, compatibility throughout the entire workflow.

Flexibility in design (scalability to complex multi-amplicon / multi-gRNA design per gene).

Predicted effect of the observed mutation on the encoded protein level.

Customized aggregation of effects per haplotype (thresholds).

Customized aggregation of alleles per effect class per locus (thresholds).

Discretizing the complex haplotype table to a simple homozygous / heterozygous LOF effect per locus per sample.

Single command line operation per module.

Traceable output (discrete LOF-call genotype table, alignments, VCF-encoded variants, predicted proteins).

Biology-driven decisions.

Integration in the SMAP workflow

../_images/SMAP_global_scheme_home_effect.png

SMAP effect-prediction is run on a reference sequence FASTA file with candidate genes, and associated GFF file with gene annotations created by SMAP target-selection, optionally a gRNA FASTA file and locus positions created by SMAP design, and a genotype call table created by SMAP haplotype-window. SMAP effect-prediction works on HiPlex data.

Guidelines for SMAP effect-prediction

These tabs provide a decision scheme to guide you to the correct parameter settings.

Answer the questions in blue according to your data and analysis objectives. See section Recommendations and guidelines for further details.

You have:
👉 a FASTA file with reference sequences.
👉 A GFF file with border positions in the reference sequence to delineate amplicon positions.
👉 A master table with relative haplotype frequencies per sample from SMAP haplotype-window.

Do you want to filter for mutations in regions of interest (ROI) within haplotype sequences (*e.g.* based on gRNA position)?

Yes, I want to consider mutations only in a specific range around the gRNA cut site.

I must therefore:

👉 provide a GFF file with the coordinates of the gRNAs option -u.

👉 define the lower bounds option -r and upper bounds option -s around the cutsite, as nucleotide distance.

and

👉 define an offset for the cut site position option -f relative to the gRNA 5’ end
or
👉 use a predefined offset by selecting a CAS protein option -p.

This will define the region of interest (ROI) searched for mutations. Any mutation that overlaps with at least one nucleotide to the ROI is retained. Mutations outside the ROI are considered as reference sequence and ignored for the prediction of the protein sequence (only the sequences corresponding to the ROI are substituted to the reference sequence before ORF translation). Haplotypes with only mutations outside the ROI are collapsed with the reference haplotype during aggregation.

Check out the schemes below for the definition of lower -r and upper bounds -s, offset -f or -p, and ROI for gRNAs located on the forward and/or reverse strand -u.

../_images/HIW_collect_ROI_CRISPR_single_guide_forward.png

Do you want to predict the effect of mutations in the ROI on the encoded protein?

Yes, I want to predict the encoded protein by substitution of the haplotype sequence in the corresponding reference sequence, and translation of the resulting ORF.

I must therefore:
👉 provide a GFF file with CDS annotations of the reference sequences option -a. CDS features must be located on the positive strand.

Do you want to aggregate the haplotype frequencies based on their effect on the encoded protein?

Yes, I want to aggregate the haplotype frequencies by predicted effect class.
e.g. create the sum of frequencies of all haplotypes leading to major effects, and aggregate the frequencies of all other haplotypes with minor or no effect as reference haplotype.

I must therefore:
👉 set a threshold for the percentage protein sequence identity between the mutated and reference protein. Haplotypes below the threshold are considered having a major effect and their relative frequencies are summed.

Do you want to discretize the aggregated frequencies into discrete calls?

Yes, I want to discretize the aggregated frequencies into categorical groups (i.e. genotype calls).

I must therefore:
👉 set the frequency bounds option -i to transform frequency data of haplotypes into discrete genotype calls (homozygous reference, heterozygous, homozygous mutated at the predicted protein effect class (minor, major effect)).
👉 set discrete calls option -e to get binary presence/absence data.

No, I do not want to predict the effect of alternative haplotypes on the encoded protein.

I must therefore:
👉 disable this function --disable_protein_prediction.
👉 consider ‘annotate.tsv’ and ‘collapse.tsv’ as main outputs.

No, I want to consider mutations in the entire haplotype region (corresponding to the reference sequence between the borders).

Do you want to predict the effect of haplotype mutations on the encoded protein?

Yes, I want to predict the encoded protein by substitution of the entire haplotype sequence in the corresponding reference sequence.

I must therefore:
👉 provide a GFF file with CDS annotations of the reference sequences option -a. CDS features must be located on the positive strand.

Do you want to aggregate the haplotype frequencies based on their effect on the encoded protein?

Yes, I want to aggregate the haplotype frequencies by predicted effect class.
e.g. create the sum of frequencies of all haplotypes leading to major effects, and aggregate the frequencies of all other haplotypes with minor or no effect as reference haplotype.

I must therefore:
👉 set a threshold for the percentage protein sequence identity between the mutated and reference protein. Haplotypes below the threshold are considered having a major effect and their relative frequencies are summed.

Do you want to discretize the aggregated frequencies into discrete calls?

Yes, I want to discretize the aggregated frequencies into categorical groups (i.e. genotype calls).

I must therefore:
👉 set the frequency bounds option -i to transform frequency data of haplotypes into discrete genotype calls (homozygous reference, heterozygous, homozygous mutated at the predicted protein effect class (minor, major effect)).
👉 set discrete calls option -e to get binary presence/absence data.

No, I do not want to predict the effect of alternative haplotypes on the encoded protein.

I must therefore:
👉 disable that function using option --disable_protein_prediction.
👉 consider ‘annotate.tsv’ and ‘collapse.tsv’ as main output.

Commands & options

Mandatory options for SMAP effect-prediction

It is mandatory to specify the files with the haplotype frequency table, the associated reference sequence, the set of gRNA sequences and GFF with positional information of CDS.

Input and output information: It is mandatory to specify the files with the haplotype frequency table, the associated reference sequence, the set of gRNA sequences, and a GFF3 with structural gene annotation. First, the haplotype frequency table should be generated using SMAP haplotype-window. Second, the same reference sequence that was used to generate the haplotype frequency table with SMAP haplotype-window must be provided to SMAP effect-prediction. Third, haplotype calling occurred within a ‘window’, defined by two borders (typically the 10 nucleotides at the 3’ of the HiPlex primers). The position of the windows are provided to SMAP effect-prediction by a GFF3 file containing the positions of these borders. A single gff entry corresponds to one border, and two borders must be linked together to form a window by using a shared NAME attribute value. All borders must be specified in the ‘+’ orientation to the reference genome. Finally, a GFF3 file defining the gene and CDS information should be provided. For your convenience, all these input files can be prepared with the modules SMAP target-selection and SMAP design.

Regarding input files, there is only one file that is considered optional: a GFF3 file of the gRNA positions. These gRNA positions allow SMAP effect-prediction to filter haplotypes to collapse those haplotypes that only contain variations outside a user-defined range around the cut site defined by the gRNA where ‘true positive’ variation resulting from CRISPR/Cas activity is expected to occur. Each gRNA should be a single gff entry, with a ‘+’ or ‘-’ orientation compared to the reference. Additionally, each gRNA should have a unique NAME attribute that specifies its target locus.

The locations of the gRNAs are not enough to specify where the Cas enzyme cuts the DNA for editing. The type of Cas protein used for the editing experiment also determines the offset relative to the position of the gRNA. Therefore, options are available to specify this offset by either using a predefined offset by using the name of the Cas9 protein, or by using a custom offset (i.e. number of nucleotides).

-u, --gRNAs ############### (str) ### .gff file containing the gRNA coordinates, must contain NAME=<> in column 9.
-g, --no_gRNA_relative_naming ## (str) ### Change the haplotype naming according to the gRNA coordinates.
-p, --cas_protein ########### (str) ### Name of the nuclease used in the experiment. Used to select a predefined offset [CAS9].
-f CAS_OFFSET, --cas_offset #### (int) ### Cas offset in number of nucleotides.

-s, --cut_site_range_upper_bound ## (str) ### Upper bound for selecting variations from a range around the cut site. Defined in the direction from the cut site towards the PAM.

-r, --cut_site_range_lower_bound ## (str) ### Lower bound for selecting variations from a range around the cut site. Defined in the direction from the cut site towards the start of the gRNA binding site.

-c, --cpu ### (str) ### Maximum number of allowed processes.

Alignment parameters: The default settings below have been determined empirically. As SMAP effect-prediction relies heavily on the alignment of haplotypes to the reference sequence, caution is advised when changing these defaults. For more information on the alignment implementation, we refer to the biopython documentation. Define the parameters to align the haplotype sequences to the reference sequence.

--match_score ##### (str) ###
--mismatch_penalty ## (str) ###
--gap_open_penalty ## (str) ###
--gap_extension #### (str) ###

Use thresholds to transform haplotype frequencies into discrete calls using fixed intervals. The assigned intervals are indicated by a running integer. This is only informative for individual samples and not for Pool-Seq data.

-e, --discrete_calls {dominant,dosage} ########## (str) ### Set to “dominant” to transform haplotype frequency values into presence(1)/absence(0) calls per allele, or “dosage” to indicate the allele copy number.

-i, --frequency_interval_bounds ################# (str) ### Frequency interval bounds for transforming haplotype frequencies into discrete calls. Custom thresholds can be defined by passing one or more space-separated values (relative frequencies in percentage). For dominant calling, one value should be specified. For dosage calling, an even total number of four or more thresholds should be specified. Default values are invoked by passing either “diploid” or “tetraploid”. The default value for dominant calling (see discrete_calls argument) is 10, both for “diploid” and “tetraploid”. For dosage calling, the default for diploids is “10, 10, 90, 90” and for tetraploids “12.5, 12.5, 37.5, 37.5, 62.5, 62.5, 87.5, 87.5”.

--disable_protein_prediction ### (str) ### Disable the estimation of the protein from the haplotypes sequences. All variations within range (-s and -r) of the cut site will be considered as relevant sequence variant with an effect. This option requires --gRNAs.

-t, --effect_threshold ####### (str) ### Threshold to determine whether a protein is affected by the haplotype variant sequence or not. For each haplotype, a protein identity score is calculated compared to the reference. Haplotypes for which the protein identity is below the effect threshold, will be marked as encoding an affected protein.For instance, a protein with 10% identity to the reference, is below an effect threshold of 50%, and will be marked as loss-of-function (LOF).

Example commands

Example command line to run SMAP effect-prediction with adjusted aggregation thresholds:

smap effect-prediction haplotype-window_genotype_table.tsv genome.fasta borders.gff local_gff_file.gff3 -u gRNAs.gff -p CAS9 -s 10 -r 20 -e dosage -i diploid -t 90

Output

SMAP effect-prediction creates two pre-aggregation tables: annotate.tsv and collapsed.tsv.

SMAP effect-prediction creates two post-aggregation tables: aggregated.tsv and discretized.tsv.

The following tabs show real experimental data of nine loci. All detected haplotypes are reported using the default settings, demonstrating how annotation and aggregation compresses the genotype call table, and discretization simplifies the calls to heterozygous/homozygous knock-out genotype calls.

Reference	Locus	Haplotypes	target	edit	start	end	SNP	INDEL	Alignment	FILTER_gRNA_INDEL	FILTER_gRNA_SNP	FILTER_gRNA	Haplotype_Name	Expected cut site	atgCheck	splicingSiteCheck	stopCodonCheck	protein_sequence	pairwiseProteinIdentity (%)	Effect	sample1	sample2	sample3	sample4	sample5	sample6	sample7	sample8
gene1	gene1_1	GGCTCTGTTCTTTTACTCGGCCCTGTTTGACGCTCTGGACACGACCACTCCAAGAGACAGCAACCAGAGGATGCT	gene1	ref	1790	1865	nan	nan	nan	nan	nan	nan	ref	1817				MGSSYDPYPSPGADDLFLYLSDLGPASPSAYLDLPPTPQPQPYPQSQQQQQGSKGPTQDMLLPYISSMLMEDDIDDTFFYDYPDNPALLQAQQSFLDILSDDASSPTTTTGTTNSSASVNHSSSDASASAPPTPAAVDSYSPAPAVQFDGFDLDPAAFFSNGANSDLMSSAFLKGMEEANKFLPSQDKLVIDLDPPDDTKRFVLPTRAAENLAPGFNAAATTVPAAVAMAVKEEEVILAALDAALGSGGVVLGRGRRNRLDDDEEDLELQRRSTKQSALQGDGDERDVFEKYIMTCPETCTEQMQQLRIAMQEEAAKEAAVAAGNGKAKGRRGGREVVDLRTLLVHCAQAVASDDRRSATELLRQIKQHASPQGDATQRLAHCFAEGLQARLAGTGSMVYQSLMAKRTSAADILQAYQLYMAAICFKRVVFVFSNNTIYNAALGKMKIHIVDYGIHYGFQWPCFLRWIADREGGPPEVRITGIDLPQPGFRPTQRIEETGRRLSKYAQQFGVPFKYQAIAASKMESIRAEDLNLDPEEVLIVNCLYQFKNLMDESVVIESPRDIVLNNIRKMRPHTFIHAIVNGSFSAPFFVTRFREALFFYSALFDALDTTTPRDSNQRMLIEENLFGRAALNVIACEGTDRVERPETYKQWQVRNQRAGLKQQPLNPDVVQQDIGTSNQEEICDASMS*	NA	False	100.0	100.0	100.0	100.0	100.0	100.0	100.0	100.0
gene2	gene2_1	AGTGCTAGGTGATGCTGCGCGAGTACTGCGAGATCTAATCACTCAAGTGGAATCTCTCAGGCAGGAACAATCTGCTCTTG	gene2	ref	3751	3831	nan	nan	nan	nan	nan	nan	ref	3795				EFPCRWGRRRRHVSPRYRLGHTSVRVGGRHTLAAPACVCSPPTLPALALHFPWQSSLVPDFLPERIRPPSIRPPVPAGLRGSSAWDQDPSRPRHPRAKDRIKARTNILGMVADTESSDSLPGSSNAASEMPANGSIHRKSQEKPPKKTHKAEREKLKRDQLNDLFVELGSMLDLDRQNTGKATVLGDAARVLRDLITQVESLRQEQSALVSERQYVSSEKNELQEENSSLKSQISELQTELCARMRSSSLSQTSIGMSDPATHQQMQMWSSIPHLSSVAMAARPASAASPLHGQEGYSADAGQAGYAPQPQPRELQLFPGSSASSSPERERSSRLGSGQATPPSLTDSLPGQLCLSLLQPSQEASGGGGGGVMSRSREERRDG*	NA	False	49.5	52.8	NA	NA	57.2	52.3	45.9	50.1
gene2	gene2_1	AGTGCTAGGTGTTGCTGCGCGAGTACTGCGAGATCTAATCACTCAAGTGGAATCTCTCAGGCAGGAGCAATCTGCTCTTG	gene2	0	3751	3831	((3762, ‘A’, ‘T’), (3817, ‘A’, ‘G’))	()	AGTGCTAGGTGATGCTGCGCGAGTACTGCGAGATCTAATCACTCAAGTGGAATCTCTCAGGCAGGAACAATCTGCTCTTG AGTGCTAGGTGTTGCTGCGCGAGTACTGCGAGATCTAATCACTCAAGTGGAATCTCTCAGGCAGGAGCAATCTGCTCTTG	nan	False	False	-31:S:A-T,24:S:A-G	3795	False	False	False	EFPCRWGRRRRHVSPRYRLGHTSVRVGGRHTLAAPACVCSPPTLPALALHFPWQSSLVPDFLPERIRPPSIRPPVPAGLRGSSAWDQDPSRPRHPRAKDRIKARTNILGMVADTESSDSLPGSSNAASEMPANGSIHRKSQEKPPKKTHKAEREKLKRDQLNDLFVELGSMLDLDRQNTGKATVLGDAARVLRDLITQVESLRQEQSALVSERQYVSSEKNELQEENSSLKSQISELQTELCARMRSSSLSQTSIGMSDPATHQQMQMWSSIPHLSSVAMAARPASAASPLHGQEGYSADAGQAGYAPQPQPRELQLFPGSSASSSPERERSSRLGSGQATPPSLTDSLPGQLCLSLLQPSQEASGGGGGGVMSRSREERRDG*	100.0	False	50.5	47.2	48.2	NA	NA	47.7	NA	49.9
gene2	gene2_1	AGTGCTAGGTGATGCTGCGCGAGTACTGCGAGATCTAATCACAAGTGGAATCTCTCAGGCAGGAACAATCTGCTCTTG	gene2	2	3751	3831	()	((3792, ‘ACT’, ‘A’),)	AGTGCTAGGTGATGCTGCGCGAGTACTGCGAGATCTAATCACTCAAGTGGAATCTCTCAGGCAGGAACAATCTGCTCTTG AGTGCTAGGTGATGCTGCGCGAGTACTGCGAGATCTAATCA–CAAGTGGAATCTCTCAGGCAGGAACAATCTGCTCTTG	True	nan	True	-1:2D:ACT-A	3795	False	False	False	EFPCRWGRRRRHVSPRYRLGHTSVRVGGRHTLAAPACVCSPPTLPALALHFPWQSSLVPDFLPERIRPPSIRPPVPAGLRGSSAWDQDPSRPRHPRAKDRIKARTNILGMVADTESSDSLPGSSNAASEMPANGSIHRKSQEKPPKKTHKAEREKLKRDQLNDLFVELGSMLDLDRQNTGKATVLGDAARVLRDLITSGISQAGTICSCIGAPICQFREE*	54.8	True	NA	NA	51.8	45.0	NA	NA	NA	NA
gene2	gene2_1	AGTGCTAGGTGTTGCTGCGCGAGTACTGCGAGATCTAATCAAAGTGGAATCTCTCAGGCAGGAGCAATCTGCTCTTG	gene2	3	3751	3831	((3762, ‘A’, ‘T’), (3817, ‘A’, ‘G’))	((3792, ‘ACTC’, ‘A’),)	AGTGCTAGGTGATGCTGCGCGAGTACTGCGAGATCTAATCACTCAAGTGGAATCTCTCAGGCAGGAACAATCTGCTCTTG AGTGCTAGGTGTTGCTGCGCGAGTACTGCGAGATCTAATCA—AAGTGGAATCTCTCAGGCAGGAGCAATCTGCTCTTG	True	False	True	-1:3D:ACTC-A,-31:S:A-T,24:S:A-G	3795	False	False	False	EFPCRWGRRRRHVSPRYRLGHTSVRVGGRHTLAAPACVCSPPTLPALALHFPWQSSLVPDFLPERIRPPSIRPPVPAGLRGSSAWDQDPSRPRHPRAKDRIKARTNILGMVADTESSDSLPGSSNAASEMPANGSIHRKSQEKPPKKTHKAEREKLKRDQLNDLFVELGSMLDLDRQNTGKATVLGDAARVLRDLIKVESLRQEQSALVSERQYVSSEKNELQEENSSLKSQISELQTELCARMRSSSLSQTSIGMSDPATHQQMQMWSSIPHLSSVAMAARPASAASPLHGQEGYSADAGQAGYAPQPQPRELQLFPGSSASSSPERERSSRLGSGQATPPSLTDSLPGQLCLSLLQPSQEASGGGGGGVMSRSREERRDG*	99.5	False	NA	NA	NA	55.0	42.8	NA	54.1	NA
gene3	gene3_1	CTGACGTGCTCACTTGCTGACATACCTAGGTACTCTGCCTACGGGGTGAAGTCTCTGTCGGACGAGCACAGCCAGCTCT	gene3	ref	3078	3157	nan	nan	nan	nan	nan	nan	ref	3121				MAMPFASLSPAADHRPSSLLPYCRAAPLSAVGEDAAAQAQQQQQHAMSGRWAARPPALFTAAQYEELEHQALIYKYLVAGVPVPPDLLLPLRRGFVYHQPALGYGPYFGKKVDPEPGRCRRTDGKKWRCSKEAAPDSKYCERHMHRGRNRSRKPVEAQLVPPPHAQQQQQQQAPAPTAGFQSHPMYPSILAGNGGGGGGVGGGAGGGGTFGLGPTSQLHMDSAAAYATAAGGGSKDLRYSAYGVKSLSDEHSQLLSGGGGMDASMDNSWRLLPSQTAATFQATSYPLFGALSGLDESTIASLPKTQREPLSFFGSDFVTPKQENQTLRPFFDEWPKSRDSWPELNEDNSLGSSATQLSISIPMAPSDFNTSSRSPNGIPSR*	NA	False	100.0	97.0	44.3	NA	48.0	NA	4.2	5.0
gene3	gene3_1	CTGACGTGCTCACGTGCTGACATACCTAGGTACTCTGCCTACGGGGTGAAGTCTCTGTCGGACGAGCACAGCCAGCTCT	gene3	0	3078	3157	((3091, ‘T’, ‘G’),)	()	CTGACGTGCTCACTTGCTGACATACCTAGGTACTCTGCCTACGGGGTGAAGTCTCTGTCGGACGAGCACAGCCAGCTCT CTGACGTGCTCACGTGCTGACATACCTAGGTACTCTGCCTACGGGGTGAAGTCTCTGTCGGACGAGCACAGCCAGCTCT	nan	False	False	28:S:T-G	3121	False	False	False	MAMPFASLSPAADHRPSSLLPYCRAAPLSAVGEDAAAQAQQQQQHAMSGRWAARPPALFTAAQYEELEHQALIYKYLVAGVPVPPDLLLPLRRGFVYHQPALGYGPYFGKKVDPEPGRCRRTDGKKWRCSKEAAPDSKYCERHMHRGRNRSRKPVEAQLVPPPHAQQQQQQQAPAPTAGFQSHPMYPSILAGNGGGGGGVGGGAGGGGTFGLGPTSQLHMDSAAAYATAAGGGSKDLRYSAYGVKSLSDEHSQLLSGGGGMDASMDNSWRLLPSQTAATFQATSYPLFGALSGLDESTIASLPKTQREPLSFFGSDFVTPKQENQTLRPFFDEWPKSRDSWPELNEDNSLGSSATQLSISIPMAPSDFNTSSRSPNGIPSR*	100.0	False	NA	3.0	NA	NA	NA	NA	NA	NA
gene3	gene3_1	CTGACGTGCTCACTTGCTGACATACCTAGGTACTCTGCCTACGGGGTGAAGTCTCTGTCGGACGAGCACATCCAGCTCT	gene3	0	3078	3157	((3148, ‘G’, ‘T’),)	()	CTGACGTGCTCACTTGCTGACATACCTAGGTACTCTGCCTACGGGGTGAAGTCTCTGTCGGACGAGCACAGCCAGCTCT CTGACGTGCTCACTTGCTGACATACCTAGGTACTCTGCCTACGGGGTGAAGTCTCTGTCGGACGAGCACATCCAGCTCT	nan	False	False	-29:S:G-T	3121	False	False	False	MAMPFASLSPAADHRPSSLLPYCRAAPLSAVGEDAAAQAQQQQQHAMSGRWAARPPALFTAAQYEELEHQALIYKYLVAGVPVPPDLLLPLRRGFVYHQPALGYGPYFGKKVDPEPGRCRRTDGKKWRCSKEAAPDSKYCERHMHRGRNRSRKPVEAQLVPPPHAQQQQQQQAPAPTAGFQSHPMYPSILAGNGGGGGGVGGGAGGGGTFGLGPTSQLHMDSAAAYATAAGGGSKDLRYSAYGVKSLSDEHSQLLSGGGGMDASMDNSWRLLPSQTAATFQATSYPLFGALSGLDESTIASLPKTQREPLSFFGSDFVTPKQENQTLRPFFDEWPKSRDSWPELNEDNSLGSSATQLSISIPMAPSDFNTSSRSPNGIPSR*	100.0	False	NA	NA	5.6	NA	NA	NA	NA	NA
gene3	gene3_1	CTGACGTACTCACTTGCTGACATACCTAGGTACTCTGCCTACGGGGTGAAGTCTCTGTCGGACGAGCACAGCCAGCTCT	gene3	0	3078	3157	((3085, ‘G’, ‘A’),)	()	CTGACGTGCTCACTTGCTGACATACCTAGGTACTCTGCCTACGGGGTGAAGTCTCTGTCGGACGAGCACAGCCAGCTCT CTGACGTACTCACTTGCTGACATACCTAGGTACTCTGCCTACGGGGTGAAGTCTCTGTCGGACGAGCACAGCCAGCTCT	nan	False	False	34:S:G-A	3121	False	False	False	MAMPFASLSPAADHRPSSLLPYCRAAPLSAVGEDAAAQAQQQQQHAMSGRWAARPPALFTAAQYEELEHQALIYKYLVAGVPVPPDLLLPLRRGFVYHQPALGYGPYFGKKVDPEPGRCRRTDGKKWRCSKEAAPDSKYCERHMHRGRNRSRKPVEAQLVPPPHAQQQQQQQAPAPTAGFQSHPMYPSILAGNGGGGGGVGGGAGGGGTFGLGPTSQLHMDSAAAYATAAGGGSKDLRYSAYGVKSLSDEHSQLLSGGGGMDASMDNSWRLLPSQTAATFQATSYPLFGALSGLDESTIASLPKTQREPLSFFGSDFVTPKQENQTLRPFFDEWPKSRDSWPELNEDNSLGSSATQLSISIPMAPSDFNTSSRSPNGIPSR*	100.0	False	NA	NA	NA	NA	4.4	NA	NA	NA
gene3	gene3_1	CTGACGTGCTCACTTGCTGACATACCTAGGTACTCTGCCTACGGGGGTGAAGTCTCTGTCGGACGAGCACAGCCAGCTCT	gene3	-1	3078	3157	()	((3120, ‘C’, ‘CG’),)	CTGACGTGCTCACTTGCTGACATACCTAGGTACTCTGCCTAC-GGGGTGAAGTCTCTGTCGGACGAGCACAGCCAGCTCT CTGACGTGCTCACTTGCTGACATACCTAGGTACTCTGCCTACGGGGGTGAAGTCTCTGTCGGACGAGCACAGCCAGCTCT	True	nan	True	-1:1I:C-CG	3121	False	False	False	MAMPFASLSPAADHRPSSLLPYCRAAPLSAVGEDAAAQAQQQQQHAMSGRWAARPPALFTAAQYEELEHQALIYKYLVAGVPVPPDLLLPLRRGFVYHQPALGYGPYFGKKVDPEPGRCRRTDGKKWRCSKEAAPDSKYCERHMHRGRNRSRKPVEAQLVPPPHAQQQQQQQAPAPTAGFQSHPMYPSILAGNGGGGGGVGGGAGGGGTFGLGPTSQLHMDSAAAYATAAGGGSKDLRYSAYGGEVSVGRAQPALVRRRRHGRVNGQLVAPVAVPNRRHVPGHKLPSVRRAERSGREHHRLAAQDAEGAPLLLRERLRDPEAGEPDAAPLLRRVAQVEGLVAGAERGQQPRLLGHPALHLHPHGALRLQHQLQIAEWNTVKVKPSIRRHTCFFFLLFFRFEPFVLRTFF*	62.6	True	NA	NA	47.9	55.5	47.6	40.3	47.5	56.0
gene3	gene3_1	CTGACGTGCTCACTTGCTGACATACCTAGGTACTCTGCCTACGTGGGTGAAGTCTCTGTCGGACGAGCACAGCCAGCTCT	gene3	-1	3078	3157	()	((3121, ‘G’, ‘GT’),)	CTGACGTGCTCACTTGCTGACATACCTAGGTACTCTGCCTACG-GGGTGAAGTCTCTGTCGGACGAGCACAGCCAGCTCT CTGACGTGCTCACTTGCTGACATACCTAGGTACTCTGCCTACGTGGGTGAAGTCTCTGTCGGACGAGCACAGCCAGCTCT	True	nan	True	-2:1I:G-GT	3121	False	False	False	MAMPFASLSPAADHRPSSLLPYCRAAPLSAVGEDAAAQAQQQQQHAMSGRWAARPPALFTAAQYEELEHQALIYKYLVAGVPVPPDLLLPLRRGFVYHQPALGYGPYFGKKVDPEPGRCRRTDGKKWRCSKEAAPDSKYCERHMHRGRNRSRKPVEAQLVPPPHAQQQQQQQAPAPTAGFQSHPMYPSILAGNGGGGGGVGGGAGGGGTFGLGPTSQLHMDSAAAYATAAGGGSKDLRYSAYVGEVSVGRAQPALVRRRRHGRVNGQLVAPVAVPNRRHVPGHKLPSVRRAERSGREHHRLAAQDAEGAPLLLRERLRDPEAGEPDAAPLLRRVAQVEGLVAGAERGQQPRLLGHPALHLHPHGALRLQHQLQIAEWNTVKVKPSIRRHTCFFFLLFFRFEPFVLRTFF*	63.1	True	NA	NA	NA	44.5	NA	NA	7.6	9.0
gene3	gene3_1	CTGACGTGCTCACTTGCTGACATACCTAGGTACTCTGCCTACTGGGTGAAGTCTCTGTCGGACGAGCACAGCCAGCTCT	gene3	0	3078	3157	((3120, ‘G’, ‘T’),)	()	CTGACGTGCTCACTTGCTGACATACCTAGGTACTCTGCCTACGGGGTGAAGTCTCTGTCGGACGAGCACAGCCAGCTCT CTGACGTGCTCACTTGCTGACATACCTAGGTACTCTGCCTACTGGGTGAAGTCTCTGTCGGACGAGCACAGCCAGCTCT	nan	True	True	-1:S:G-T	3121	False	False	False	MAMPFASLSPAADHRPSSLLPYCRAAPLSAVGEDAAAQAQQQQQHAMSGRWAARPPALFTAAQYEELEHQALIYKYLVAGVPVPPDLLLPLRRGFVYHQPALGYGPYFGKKVDPEPGRCRRTDGKKWRCSKEAAPDSKYCERHMHRGRNRSRKPVEAQLVPPPHAQQQQQQQAPAPTAGFQSHPMYPSILAGNGGGGGGVGGGAGGGGTFGLGPTSQLHMDSAAAYATAAGGGSKDLRYSAYWVKSLSDEHSQLLSGGGGMDASMDNSWRLLPSQTAATFQATSYPLFGALSGLDESTIASLPKTQREPLSFFGSDFVTPKQENQTLRPFFDEWPKSRDSWPELNEDNSLGSSATQLSISIPMAPSDFNTSSRSPNGIPSR*	99.7	False	NA	NA	NA	NA	NA	NA	NA	3.0
gene3	gene3_1	CTGACGTGCTCACTTGCTGACATACCTAGGTACTCTGCCTACGGGTGAAGTCTCTGTCGGACGAGCACAGCCAGCTCT	gene3	1	3078	3157	()	((3120, ‘CG’, ‘C’),)	CTGACGTGCTCACTTGCTGACATACCTAGGTACTCTGCCTACGGGGTGAAGTCTCTGTCGGACGAGCACAGCCAGCTCT CTGACGTGCTCACTTGCTGACATACCTAGGTACTCTGCCTAC-GGGTGAAGTCTCTGTCGGACGAGCACAGCCAGCTCT	True	nan	True	-1:1D:CG-C	3121	False	False	False	MAMPFASLSPAADHRPSSLLPYCRAAPLSAVGEDAAAQAQQQQQHAMSGRWAARPPALFTAAQYEELEHQALIYKYLVAGVPVPPDLLLPLRRGFVYHQPALGYGPYFGKKVDPEPGRCRRTDGKKWRCSKEAAPDSKYCERHMHRGRNRSRKPVEAQLVPPPHAQQQQQQQAPAPTAGFQSHPMYPSILAGNGGGGGGVGGGAGGGGTFGLGPTSQLHMDSAAAYATAAGGGSKDLRYSAYG*	63.8	True	NA	NA	NA	NA	NA	NA	24.6	22.0
gene3	gene3_1	CTGACGTGCTCACTTGCTGACATACCTAGGTACTCTGCCTACGGGTGAAGTCTCTGTCGGACGAGCCCAGCCAGCTCT	gene3	1	3078	3157	((3145, ‘A’, ‘C’),)	((3120, ‘CG’, ‘C’),)	CTGACGTGCTCACTTGCTGACATACCTAGGTACTCTGCCTACGGGGTGAAGTCTCTGTCGGACGAGCACAGCCAGCTCT CTGACGTGCTCACTTGCTGACATACCTAGGTACTCTGCCTAC-GGGTGAAGTCTCTGTCGGACGAGCCCAGCCAGCTCT	True	False	True	-1:1D:CG-C,-26:S:A-C	3121	False	False	False	MAMPFASLSPAADHRPSSLLPYCRAAPLSAVGEDAAAQAQQQQQHAMSGRWAARPPALFTAAQYEELEHQALIYKYLVAGVPVPPDLLLPLRRGFVYHQPALGYGPYFGKKVDPEPGRCRRTDGKKWRCSKEAAPDSKYCERHMHRGRNRSRKPVEAQLVPPPHAQQQQQQQAPAPTAGFQSHPMYPSILAGNGGGGGGVGGGAGGGGTFGLGPTSQLHMDSAAAYATAAGGGSKDLRYSAYG*	63.8	True	NA	NA	NA	NA	NA	NA	NA	3.0
gene3	gene3_1	CTGACGTGCTCACTTGCTGACATACCTAGGTACTCTGCCTACGGTGAAGTCTCTGTCGGACGAGCACAGCCAGCTCT	gene3	2	3078	3157	()	((3120, ‘CGG’, ‘C’),)	CTGACGTGCTCACTTGCTGACATACCTAGGTACTCTGCCTACGGGGTGAAGTCTCTGTCGGACGAGCACAGCCAGCTCT CTGACGTGCTCACTTGCTGACATACCTAGGTACTCTGCCTAC–GGTGAAGTCTCTGTCGGACGAGCACAGCCAGCTCT	True	nan	True	-1:2D:CGG-C	3121	False	False	False	MAMPFASLSPAADHRPSSLLPYCRAAPLSAVGEDAAAQAQQQQQHAMSGRWAARPPALFTAAQYEELEHQALIYKYLVAGVPVPPDLLLPLRRGFVYHQPALGYGPYFGKKVDPEPGRCRRTDGKKWRCSKEAAPDSKYCERHMHRGRNRSRKPVEAQLVPPPHAQQQQQQQAPAPTAGFQSHPMYPSILAGNGGGGGGVGGGAGGGGTFGLGPTSQLHMDSAAAYATAAGGGSKDLRYSAYGEVSVGRAQPALVRRRRHGRVNGQLVAPVAVPNRRHVPGHKLPSVRRAERSGREHHRLAAQDAEGAPLLLRERLRDPEAGEPDAAPLLRRVAQVEGLVAGAERGQQPRLLGHPALHLHPHGALRLQHQLQIAEWNTVKVKPSIRRHTCFFFLLFFRFEPFVLRTFF*	62.5	True	NA	NA	2.2	NA	NA	59.7	4.2	2.0
gene3	gene3_1	CTGACGTGCTCACTTGCTGACATACCTAGGTACTCTGCCTACGTGAAGTCTCTGTCGGACGAGCACAGCCAGCTCT	gene3	3	3078	3157	()	((3120, ‘CGGG’, ‘C’),)	CTGACGTGCTCACTTGCTGACATACCTAGGTACTCTGCCTACGGGGTGAAGTCTCTGTCGGACGAGCACAGCCAGCTCT CTGACGTGCTCACTTGCTGACATACCTAGGTACTCTGCCTAC—GTGAAGTCTCTGTCGGACGAGCACAGCCAGCTCT	True	nan	True	-1:3D:CGGG-C	3121	False	False	False	MAMPFASLSPAADHRPSSLLPYCRAAPLSAVGEDAAAQAQQQQQHAMSGRWAARPPALFTAAQYEELEHQALIYKYLVAGVPVPPDLLLPLRRGFVYHQPALGYGPYFGKKVDPEPGRCRRTDGKKWRCSKEAAPDSKYCERHMHRGRNRSRKPVEAQLVPPPHAQQQQQQQAPAPTAGFQSHPMYPSILAGNGGGGGGVGGGAGGGGTFGLGPTSQLHMDSAAAYATAAGGGSKDLRYSAYVKSLSDEHSQLLSGGGGMDASMDNSWRLLPSQTAATFQATSYPLFGALSGLDESTIASLPKTQREPLSFFGSDFVTPKQENQTLRPFFDEWPKSRDSWPELNEDNSLGSSATQLSISIPMAPSDFNTSSRSPNGIPSR*	99.7	False	NA	NA	NA	NA	NA	NA	4.2	NA
gene3	gene3_1	CTGACGTGCTCACTTGCTGACATACCTAGGTACTCTGCCTACGAAGTCTCTGTCGGACGAGCACAGCCAGCTCT	gene3	5	3078	3157	()	((3120, ‘CGGGGT’, ‘C’),)	CTGACGTGCTCACTTGCTGACATACCTAGGTACTCTGCCTACGGGGTGAAGTCTCTGTCGGACGAGCACAGCCAGCTCT CTGACGTGCTCACTTGCTGACATACCTAGGTACTCTGCCTAC—–GAAGTCTCTGTCGGACGAGCACAGCCAGCTCT	True	nan	True	-1:5D:CGGGGT-C	3121	False	False	False	MAMPFASLSPAADHRPSSLLPYCRAAPLSAVGEDAAAQAQQQQQHAMSGRWAARPPALFTAAQYEELEHQALIYKYLVAGVPVPPDLLLPLRRGFVYHQPALGYGPYFGKKVDPEPGRCRRTDGKKWRCSKEAAPDSKYCERHMHRGRNRSRKPVEAQLVPPPHAQQQQQQQAPAPTAGFQSHPMYPSILAGNGGGGGGVGGGAGGGGTFGLGPTSQLHMDSAAAYATAAGGGSKDLRYSAYEVSVGRAQPALVRRRRHGRVNGQLVAPVAVPNRRHVPGHKLPSVRRAERSGREHHRLAAQDAEGAPLLLRERLRDPEAGEPDAAPLLRRVAQVEGLVAGAERGQQPRLLGHPALHLHPHGALRLQHQLQIAEWNTVKVKPSIRRHTCFFFLLFFRFEPFVLRTFF*	62.6	True	NA	NA	NA	NA	NA	NA	1.7	NA
gene3	gene3_1	CTGACGTGCTCACTTGCTGACATACCTAGGTACTCTGCCTAAGTCTCTGTCGGACGAGCACAGCCAGCTCT	gene3	8	3078	3157	()	((3118, ‘TACGGGGTG’, ‘T’),)	CTGACGTGCTCACTTGCTGACATACCTAGGTACTCTGCCTACGGGGTGAAGTCTCTGTCGGACGAGCACAGCCAGCTCT CTGACGTGCTCACTTGCTGACATACCTAGGTACTCTGCCT——–AAGTCTCTGTCGGACGAGCACAGCCAGCTCT	True	nan	True	1:8D:TACGGGGTG-T	3121	False	False	False	MAMPFASLSPAADHRPSSLLPYCRAAPLSAVGEDAAAQAQQQQQHAMSGRWAARPPALFTAAQYEELEHQALIYKYLVAGVPVPPDLLLPLRRGFVYHQPALGYGPYFGKKVDPEPGRCRRTDGKKWRCSKEAAPDSKYCERHMHRGRNRSRKPVEAQLVPPPHAQQQQQQQAPAPTAGFQSHPMYPSILAGNGGGGGGVGGGAGGGGTFGLGPTSQLHMDSAAAYATAAGGGSKDLRYSA*	63.3	True	NA	NA	NA	NA	NA	NA	2.5	NA
gene3	gene3_1	CTGACGTGCTCACTTGCTGACATACCTAGGTACTCTGCCTACGTCTGTCGGACGAGCACAGCCAGCTCT	gene3	10	3078	3157	()	((3121, ‘GGGGTGAAGTC’, ‘G’),)	CTGACGTGCTCACTTGCTGACATACCTAGGTACTCTGCCTACGGGGTGAAGTCTCTGTCGGACGAGCACAGCCAGCTCT CTGACGTGCTCACTTGCTGACATACCTAGGTACTCTGCCTACG———-TCTGTCGGACGAGCACAGCCAGCTCT	True	nan	True	-2:10D:GGGGTGAAGTC-G	3121	False	False	False	MAMPFASLSPAADHRPSSLLPYCRAAPLSAVGEDAAAQAQQQQQHAMSGRWAARPPALFTAAQYEELEHQALIYKYLVAGVPVPPDLLLPLRRGFVYHQPALGYGPYFGKKVDPEPGRCRRTDGKKWRCSKEAAPDSKYCERHMHRGRNRSRKPVEAQLVPPPHAQQQQQQQAPAPTAGFQSHPMYPSILAGNGGGGGGVGGGAGGGGTFGLGPTSQLHMDSAAAYATAAGGGSKDLRYSAYVCRTSTASSCPAAAAWTRQWTTRGACCRPKPPPRSRPQATLCSAR*	69.3	True	NA	NA	NA	NA	47.6	NA	NA	NA
gene3	gene3_1	CTGACGTTGCTGAAGTCTCTGTCGGACGAGCACAGCCAGCTCT	gene3	36	3078	3157	()	((3085, ‘TGCTCACTTGCTGACATACCTAGGTACTC’, ‘T’), (3116, ‘CCTACGGGG’, ‘C’))	CTGACGTGCTCACTTGCTGACATACCTAGGTACTCTGCCTACGGGGTGAAGTCTCTGTCGGACGAGCACAGCCAGCTCT CTGACGT—————————-TGC——–TGAAGTCTCTGTCGGACGAGCACAGCCAGCTCT	True	nan	True	34:28D:TGCTCACTTGCTGACATACCTAGGTACTC-T,3:8D:CCTACGGGG-C	3121	False	True	False	MAMPFASLSPAADHRPSSLLPYCRAAPLSAVGEDAAAQAQQQQQHAMSGRWAARPPALFTAAQYEELEHQALIYKYLVAGVPVPPDLLLPLRRGFVYHQPALGYGPYFGKKVDPEPGRCRRTDGKKWRCSKEAAPDSKYCERHMHRGRNRSRKPVEAQLVPPPHAQQQQQQQAPAPTAGFQSHPMYPSILAGNGGGGGGVGGGAGGGGTFGLGPTSQLHMDSAAAYATAAGGGSKDLX*	62.2	True	NA	NA	NA	NA	NA	NA	3.5	NA
gene4	gene4_1	GATGGTGTTCTTGTGATGAAGGGTTGGGTCTGTGCTCAGGTGCCAGCAAGATGCAGGGTGTGTTGTCGAGGGTGAGGA	gene4	ref	827	905	nan	nan	nan	nan	nan	nan	ref	861				MEGGQDVFLGAAARAPPPPPSCPFHGSATATRSGGAQMLSFSSNGVAGLGLCSGASKMQGVLSRVRRPFTPTQWMELEHQALIYKHFAVNAPVPSSLLLPIKRSLNPWSSLGSSSLGWAPFRSGSADAEPGRCRRTDGKKWRCSRDAVGDQKYCERHIKRGCHRSRKHVEGRKATPTTADPTMAVSGGSLLHSHAVAWQQQGKSSAANVTDPFSLGSNRNLLDKQNLGDQFSISTSMDSFDFSSSHSSPNQAKVAFSPVAMQHEHDQLYLVHGAGSSAENVNKSQDGQLLVSRETIDDGPLGEVFKGKSCQSASADILTDHWTSTRDLRPPTGILQMSSSNTVPAENHTSNSSYLMARMANSQTVPTLH*	NA	False	100.0	98.8	48.3	64.8	98.4	98.7	53.6	41.9
gene4	gene4_1	GATGGTGTTCTTGTGATGAAGGGTTGGGTCTGTGCTCAGGTGCCAGCAAGATGCAGGGTGTGTTGTCGAGGGTGAGGAGAACCT	gene4	-6	827	905	()	((78, ‘A——’, ‘AGAACCT’),)	GATGGTGTTCTTGTGATGAAGGGTTGGGTCTGTGCTCAGGTGCCAGCAAGATGCAGGGTGTGTTGTCGAGGGTGAGGA—— GATGGTGTTCTTGTGATGAAGGGTTGGGTCTGTGCTCAGGTGCCAGCAAGATGCAGGGTGTGTTGTCGAGGGTGAGGAGAACCT	False	nan	False	-781:0I:A——-AGAACCT	861	False	False	False	MEGGQDVFLGAAARAPPPPPSCPFHGSATATRSGGAQMLSFSSNGVAGLGLCSGASKMQGVLSRVRRPFTPTQWMELEHQALIYKHFAVNAPVPSSLLLPIKRSLNPWSSLGSSSLGWAPFRSGSADAEPGRCRRTDGKKWRCSRDAVGDQKYCERHIKRGCHRSRKHVEGRKATPTTADPTMAVSGGSLLHSHAVAWQQQGKSSAANVTDPFSLGSNRNLLDKQNLGDQFSISTSMDSFDFSSSHSSPNQAKVAFSPVAMQHEHDQLYLVHGAGSSAENVNKSQDGQLLVSRETIDDGPLGEVFKGKSCQSASADILTDHWTSTRDLRPPTGILQMSSSNTVPAENHTSNSSYLMARMANSQTVPTLH*	100.0	False	NA	1.2	NA	NA	1.6	1.3	NA	NA
gene4	gene4_1	GATGGTGTTCTTGTGATGAAGGGTTGGGTCTGTGACTCAGGTGCCAGCAAGATGCAGGGTGTGTTGTCGAGGGTGAGGA	gene4	-1	827	905	()	((861, ‘G’, ‘GA’),)	GATGGTGTTCTTGTGATGAAGGGTTGGGTCTGTG-CTCAGGTGCCAGCAAGATGCAGGGTGTGTTGTCGAGGGTGAGGA GATGGTGTTCTTGTGATGAAGGGTTGGGTCTGTGACTCAGGTGCCAGCAAGATGCAGGGTGTGTTGTCGAGGGTGAGGA	True	nan	True	2:1I:G-GA	861	False	False	False	MEGGQDVFLGAAARAPPPPPSCPFHGSATATRSGGAQMLSFSSNGVAGLGL*	13.8	True	NA	NA	NA	NA	NA	NA	NA	1.5
gene4	gene4_1	GATGGTGTTCTTGTGATGAAGGGTTGGGTCTGTGTCTCAGGTGCCAGCAAGATGCAGGGTGTGTTGTCGAGGGTGAGGA	gene4	-1	827	905	()	((861, ‘G’, ‘GT’),)	GATGGTGTTCTTGTGATGAAGGGTTGGGTCTGTG-CTCAGGTGCCAGCAAGATGCAGGGTGTGTTGTCGAGGGTGAGGA GATGGTGTTCTTGTGATGAAGGGTTGGGTCTGTGTCTCAGGTGCCAGCAAGATGCAGGGTGTGTTGTCGAGGGTGAGGA	True	nan	True	2:1I:G-GT	861	False	False	False	MEGGQDVFLGAAARAPPPPPSCPFHGSATATRSGGAQMLSFSSNGVAGLGLCLRCQQDAGCVVEGEEALHSDAVDGAGAPGPDLQALRCECPCAVQLAPPYQKKPQSMEQPWLQLIGMGTISFRLC*	23.6	True	NA	NA	51.7	35.2	NA	NA	46.4	55.3
gene4	gene4_1	GATGGTGTTCTTGTGATGAAGGGTTGGGTCTGTCTCAGGTGCCAGCAAGATGCAGGGTGTGTTGTCGAGGGTGAGGA	gene4	1	827	905	()	((860, ‘TG’, ‘T’),)	GATGGTGTTCTTGTGATGAAGGGTTGGGTCTGTGCTCAGGTGCCAGCAAGATGCAGGGTGTGTTGTCGAGGGTGAGGA GATGGTGTTCTTGTGATGAAGGGTTGGGTCTGT-CTCAGGTGCCAGCAAGATGCAGGGTGTGTTGTCGAGGGTGAGGA	True	nan	True	1:1D:TG-T	861	False	False	False	MEGGQDVFLGAAARAPPPPPSCPFHGSATATRSGGAQMLSFSSNGVAGLGLSQVPARCRVCCRG*	16.5	True	NA	NA	NA	NA	NA	NA	NA	1.3
gene5	gene5_1	CGCGCTGCCCATCCCTCCCCACCAATCCCTCCTGCTGGTAAGCGCGCGGCCGGCGGAGAGCCGGCTGGGACTGGCACTGGGA	gene5	ref	1190	1272	nan	nan	nan	nan	nan	nan	ref	1212				MSSSSSSSSAATVFPPSPQLPPPLLVENLPPLHQLTPPVAAAAAPASEQLCYVHCHFCDTVLVVSVPTSSLFKTVTVRCGHCSSLLTVNMRGLLFPGTPANTAAAAAAAPPPPPAAVTSTTATITTAPAPPPATSVNNNGQFHFIPHSLDLALPIPPHQSLLLDEISSAANPSLQLLEQHGLGGMIPSGRNAAALHPHPPQPQPPAAGKGAKEPSPRANSAINRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLMPDHQGPKKTSLLPQDHQRSDGGGLLKEGLYAAAANMGVAPY*	NA	False	100.0	100.0	38.3	45.4	43.7	42.8	4.5	2.2
gene5	gene5_1	CGCGCTGCCCATCCCTCCCCACACAATCCCTCCTGCTGGTAAGCGCGCGGCCGGCGGAGAGCCGGCTGGGACTGGCACTGGGA	gene5	-1	1190	1272	()	((1212, ‘C’, ‘CA’),)	CGCGCTGCCCATCCCTCCCCAC-CAATCCCTCCTGCTGGTAAGCGCGCGGCCGGCGGAGAGCCGGCTGGGACTGGCACTGGGA CGCGCTGCCCATCCCTCCCCACACAATCCCTCCTGCTGGTAAGCGCGCGGCCGGCGGAGAGCCGGCTGGGACTGGCACTGGGA	True	nan	True	-2:1I:C-CA	1212	False	False	False	MSSSSSSSSAATVFPPSPQLPPPLLVENLPPLHQLTPPVAAAAAPASEQLCYVHCHFCDTVLVVSVPTSSLFKTVTVRCGHCSSLLTVNMRGLLFPGTPANTAAAAAAAPPPPPAAVTSTTATITTAPAPPPATSVNNNGQFHFIPHSLDLALPIPPHTIPPAGRDIQRREPEPAVAGAARPRRHDPQRQERGRAAPAPAPAPAARSG*	57.4	True	NA	NA	NA	NA	NA	NA	NA	1.7
gene5	gene5_1	CGCGCTGCCCATCCCTCCCCACTCAATCCCTCCTGCTGGTAAGCGCGCGGCCGGCGGAGAGCCGGCTGGGACTGGCACTGGGA	gene5	-1	1190	1272	()	((1212, ‘C’, ‘CT’),)	CGCGCTGCCCATCCCTCCCCAC-CAATCCCTCCTGCTGGTAAGCGCGCGGCCGGCGGAGAGCCGGCTGGGACTGGCACTGGGA CGCGCTGCCCATCCCTCCCCACTCAATCCCTCCTGCTGGTAAGCGCGCGGCCGGCGGAGAGCCGGCTGGGACTGGCACTGGGA	True	nan	True	-2:1I:C-CT	1212	False	False	False	MSSSSSSSSAATVFPPSPQLPPPLLVENLPPLHQLTPPVAAAAAPASEQLCYVHCHFCDTVLVVSVPTSSLFKTVTVRCGHCSSLLTVNMRGLLFPGTPANTAAAAAAAPPPPPAAVTSTTATITTAPAPPPATSVNNNGQFHFIPHSLDLALPIPPHSIPPAGRDIQRREPEPAVAGAARPRRHDPQRQERGRAAPAPAPAPAARSG*	57.4	True	NA	NA	NA	NA	NA	NA	1.2	3.0
gene5	gene5_1	CGCGCTGCCCATCCCTCCCCACAATCCCTCCTGCTGGTAAGCGCGCGGCCGGCGGAGAGCCGGCTGGGACTGGCACTGGGA	gene5	1	1190	1272	()	((1211, ‘AC’, ‘A’),)	CGCGCTGCCCATCCCTCCCCACCAATCCCTCCTGCTGGTAAGCGCGCGGCCGGCGGAGAGCCGGCTGGGACTGGCACTGGGA CGCGCTGCCCATCCCTCCCCA-CAATCCCTCCTGCTGGTAAGCGCGCGGCCGGCGGAGAGCCGGCTGGGACTGGCACTGGGA	True	nan	True	-1:1D:AC-A	1212	False	False	False	MSSSSSSSSAATVFPPSPQLPPPLLVENLPPLHQLTPPVAAAAAPASEQLCYVHCHFCDTVLVVSVPTSSLFKTVTVRCGHCSSLLTVNMRGLLFPGTPANTAAAAAAAPPPPPAAVTSTTATITTAPAPPPATSVNNNGQFHFIPHSLDLALPIPPHNPSCWTRYPAPRTRACSCWSSTASAA*	53.9	True	NA	NA	2.1	NA	NA	NA	12.3	18.5
gene5	gene5_1	CGCGCTGCCCATCCCTCCCCACATCCCTCCTGCTGGTAAGCGCGCGGCCGGCGGAGAGCCGGCTGGGACTGGCACTGGGA	gene5	2	1190	1272	()	((1212, ‘CCA’, ‘C’),)	CGCGCTGCCCATCCCTCCCCACCAATCCCTCCTGCTGGTAAGCGCGCGGCCGGCGGAGAGCCGGCTGGGACTGGCACTGGGA CGCGCTGCCCATCCCTCCCCAC–ATCCCTCCTGCTGGTAAGCGCGCGGCCGGCGGAGAGCCGGCTGGGACTGGCACTGGGA	True	nan	True	-2:2D:CCA-C	1212	False	False	False	MSSSSSSSSAATVFPPSPQLPPPLLVENLPPLHQLTPPVAAAAAPASEQLCYVHCHFCDTVLVVSVPTSSLFKTVTVRCGHCSSLLTVNMRGLLFPGTPANTAAAAAAAPPPPPAAVTSTTATITTAPAPPPATSVNNNGQFHFIPHSLDLALPIPPHIPPAGRDIQRREPEPAVAGAARPRRHDPQRQERGRAAPAPAPAPAARSG*	57.4	True	NA	NA	NA	NA	NA	NA	6.0	4.3
gene5	gene5_1	CGCGCTGCCCATCCCTCCCCAATCCCTCCTGCTGGTAAGCGCGCGGCCGGCGGAGAGCCGGCTGGGACTGGCACTGGGA	gene5	3	1190	1272	()	((1208, ‘CCCA’, ‘C’),)	CGCGCTGCCCATCCCTCCCCACCAATCCCTCCTGCTGGTAAGCGCGCGGCCGGCGGAGAGCCGGCTGGGACTGGCACTGGGA CGCGCTGCCCATCCCTCC—CCAATCCCTCCTGCTGGTAAGCGCGCGGCCGGCGGAGAGCCGGCTGGGACTGGCACTGGGA	True	nan	True	2:3D:CCCA-C	1212	False	False	False	MSSSSSSSSAATVFPPSPQLPPPLLVENLPPLHQLTPPVAAAAAPASEQLCYVHCHFCDTVLVVSVPTSSLFKTVTVRCGHCSSLLTVNMRGLLFPGTPANTAAAAAAAPPPPPAAVTSTTATITTAPAPPPATSVNNNGQFHFIPHSLDLALPIPPQSLLLDEISSAANPSLQLLEQHGLGGMIPSGRNAAALHPHPPQPQPPAAGKGAKEPSPRANSAINRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLMPDHQGPKKTSLLPQDHQRSDGGGLLKEGLYAAAANMGVAPY*	99.7	False	NA	NA	NA	NA	NA	NA	1.7	45.5
gene5	gene5_1	CGCGCTGCCCATCCCTCCCCACTCCCTCCTGCTGGTAAGCGCGCGGCCGGCGGAGAGCCGGCTGGGACTGGCACTGGGA	gene5	3	1190	1272	()	((1212, ‘CCAA’, ‘C’),)	CGCGCTGCCCATCCCTCCCCACCAATCCCTCCTGCTGGTAAGCGCGCGGCCGGCGGAGAGCCGGCTGGGACTGGCACTGGGA CGCGCTGCCCATCCCTCCCCAC—TCCCTCCTGCTGGTAAGCGCGCGGCCGGCGGAGAGCCGGCTGGGACTGGCACTGGGA	True	nan	True	-2:3D:CCAA-C	1212	False	False	False	MSSSSSSSSAATVFPPSPQLPPPLLVENLPPLHQLTPPVAAAAAPASEQLCYVHCHFCDTVLVVSVPTSSLFKTVTVRCGHCSSLLTVNMRGLLFPGTPANTAAAAAAAPPPPPAAVTSTTATITTAPAPPPATSVNNNGQFHFIPHSLDLALPIPPHSLLLDEISSAANPSLQLLEQHGLGGMIPSGRNAAALHPHPPQPQPPAAGKGAKEPSPRANSAINRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLMPDHQGPKKTSLLPQDHQRSDGGGLLKEGLYAAAANMGVAPY*	99.7	False	NA	NA	NA	54.6	NA	NA	1.9	2.3
gene5	gene5_1	CGCGCTGCCCATCCCTCCCCACCCCTCCTGCTGGTAAGCGCGCGGCCGGCGGAGAGCCGGCTGGGACTGGCACTGGGA	gene5	4	1190	1272	()	((1212, ‘CCAAT’, ‘C’),)	CGCGCTGCCCATCCCTCCCCACCAATCCCTCCTGCTGGTAAGCGCGCGGCCGGCGGAGAGCCGGCTGGGACTGGCACTGGGA CGCGCTGCCCATCCCTCCCCAC—-CCCTCCTGCTGGTAAGCGCGCGGCCGGCGGAGAGCCGGCTGGGACTGGCACTGGGA	True	nan	True	-2:4D:CCAAT-C	1212	False	False	False	MSSSSSSSSAATVFPPSPQLPPPLLVENLPPLHQLTPPVAAAAAPASEQLCYVHCHFCDTVLVVSVPTSSLFKTVTVRCGHCSSLLTVNMRGLLFPGTPANTAAAAAAAPPPPPAAVTSTTATITTAPAPPPATSVNNNGQFHFIPHSLDLALPIPPHPSCWTRYPAPRTRACSCWSSTASAA*	53.6	True	NA	NA	NA	NA	NA	NA	NA	21.3
gene5	gene5_1	CGCGCTGCCCATCCCTCCCCACCCTCCTGCTGGTAAGCGCGCGGCCGGCGGAGAGCCGGCTGGGACTGGCACTGGGA	gene5	5	1190	1272	()	((1211, ‘ACCAAT’, ‘A’),)	CGCGCTGCCCATCCCTCCCCACCAATCCCTCCTGCTGGTAAGCGCGCGGCCGGCGGAGAGCCGGCTGGGACTGGCACTGGGA CGCGCTGCCCATCCCTCCCCA—–CCCTCCTGCTGGTAAGCGCGCGGCCGGCGGAGAGCCGGCTGGGACTGGCACTGGGA	True	nan	True	-1:5D:ACCAAT-A	1212	False	False	False	MSSSSSSSSAATVFPPSPQLPPPLLVENLPPLHQLTPPVAAAAAPASEQLCYVHCHFCDTVLVVSVPTSSLFKTVTVRCGHCSSLLTVNMRGLLFPGTPANTAAAAAAAPPPPPAAVTSTTATITTAPAPPPATSVNNNGQFHFIPHSLDLALPIPPHPPAGRDIQRREPEPAVAGAARPRRHDPQRQERGRAAPAPAPAPAARSG*	57.1	True	NA	NA	NA	NA	NA	NA	1.2	1.2
gene5	gene5_1	CGCGCTGCCCATCCCTCCCCACGCGCGGCCGGCGGAGAGCCGGCTGGGACTGGCACTGGGA	gene5	21	1190	1272	()	((1211, ‘ACCAATCCCTCCTGCTGGTAAG’, ‘A’),)	CGCGCTGCCCATCCCTCCCCACCAATCCCTCCTGCTGGTAAGCGCGCGGCCGGCGGAGAGCCGGCTGGGACTGGCACTGGGA CGCGCTGCCCATCCCTCCCCA———————CGCGCGGCCGGCGGAGAGCCGGCTGGGACTGGCACTGGGA	True	nan	True	-1:21D:ACCAATCCCTCCTGCTGGTAAG-A	1212	False	True	False	MSSSSSSSSAATVFPPSPQLPPPLLVENLPPLHQLTPPVAAAAAPASEQLCYVHCHFCDTVLVVSVPTSSLFKTVTVRCGHCSSLLTVNMRGLLFPGTPANTAAAAAAAPPPPPAAVTSTTATITTAPAPPPATSVNNNGQFHFIPHSLDLALPIPPX*	49.2	True	NA	NA	59.6	NA	56.3	57.2	71.2	NA
gene6	gene6_1	GATGGAGGGAGACGACTTGTCATCCTTGTCGCCATCACCGGTCCCGTACATTTTCGGTGGTGGGTTGAGGGGAAGGA	gene6	ref	704	781	nan	nan	nan	nan	nan	nan	ref	741				MDFPGGSGRRPQQQEPEHLPPMTPLPLARQGSVYSLTFDEFQSSLGGAAKDFGSMNMDELLRSIWSAEEVHSVAAASASAADHAHAAARGPVSIQHQGSLTLPRTLSQKTVDEVWRDLTCVGGGPSSGSAAPAAPPPPAQRHPTLGEITLEEFLVRAGVVREDMTAPPPVPPAPVCPAPAPRPPVLFPHGNVLAPLVPPLQFGNGFVSGAVGQQRGGPVPPAVSPRPVTASAFGKMEGDDLSSLSPSPVPYIFGGGLRGRKPPAMEKVVERRQRRMIKNRESAARSRQRKQKNPHGTGARLNGDGVAVTSVFGLDGEDHREGDQRRPKEAAEAHERSREARDVTRQKTGEYTDASREAAQEARDRSRATAQEGRHRRQGEGGQGRGRGHSSATRIWR*	NA	False	100.0	96.7	52.6	NA	100.0	50.2	100.0	100.0
gene6	gene6_1	GATGGAGGGAGACGACTTGTCATCCTTGTCGCCATCACCGGCCCCGTACATTTTCGGTGGTGGGTTGAGGGGAAGGA	gene6	0	704	781	((745, ‘T’, ‘C’),)	()	GATGGAGGGAGACGACTTGTCATCCTTGTCGCCATCACCGGTCCCGTACATTTTCGGTGGTGGGTTGAGGGGAAGGA GATGGAGGGAGACGACTTGTCATCCTTGTCGCCATCACCGGCCCCGTACATTTTCGGTGGTGGGTTGAGGGGAAGGA	nan	True	True	-6:S:T-C	741	False	False	False	MDFPGGSGRRPQQQEPEHLPPMTPLPLARQGSVYSLTFDEFQSSLGGAAKDFGSMNMDELLRSIWSAEEVHSVAAASASAADHAHAAARGPVSIQHQGSLTLPRTLSQKTVDEVWRDLTCVGGGPSSGSAAPAAPPPPAQRHPTLGEITLEEFLVRAGVVREDMTAPPPVPPAPVCPAPAPRPPVLFPHGNVLAPLVPPLQFGNGFVSGAVGQQRGGPVPPAVSPRPVTASAFGKMEGDDLSSLSPSPAPYIFGGGLRGRKPPAMEKVVERRQRRMIKNRESAARSRQRKQKNPHGTGARLNGDGVAVTSVFGLDGEDHREGDQRRPKEAAEAHERSREARDVTRQKTGEYTDASREAAQEARDRSRATAQEGRHRRQGEGGQGRGRGHSSATRIWR*	99.7	False	NA	1.1	NA	NA	NA	NA	NA	NA
gene6	gene6_1	GATGGAGGGAGACGACTTGTCATCCTTGTCGCCATCACCGGTCCCATACATTTTCGGTGGTGGGTTGAGGGGAAGGA	gene6	0	704	781	((749, ‘G’, ‘A’),)	()	GATGGAGGGAGACGACTTGTCATCCTTGTCGCCATCACCGGTCCCGTACATTTTCGGTGGTGGGTTGAGGGGAAGGA GATGGAGGGAGACGACTTGTCATCCTTGTCGCCATCACCGGTCCCATACATTTTCGGTGGTGGGTTGAGGGGAAGGA	nan	True	True	-10:S:G-A	741	False	False	False	MDFPGGSGRRPQQQEPEHLPPMTPLPLARQGSVYSLTFDEFQSSLGGAAKDFGSMNMDELLRSIWSAEEVHSVAAASASAADHAHAAARGPVSIQHQGSLTLPRTLSQKTVDEVWRDLTCVGGGPSSGSAAPAAPPPPAQRHPTLGEITLEEFLVRAGVVREDMTAPPPVPPAPVCPAPAPRPPVLFPHGNVLAPLVPPLQFGNGFVSGAVGQQRGGPVPPAVSPRPVTASAFGKMEGDDLSSLSPSPVPYIFGGGLRGRKPPAMEKVVERRQRRMIKNRESAARSRQRKQKNPHGTGARLNGDGVAVTSVFGLDGEDHREGDQRRPKEAAEAHERSREARDVTRQKTGEYTDASREAAQEARDRSRATAQEGRHRRQGEGGQGRGRGHSSATRIWR*	100.0	False	NA	1.1	NA	NA	NA	NA	NA	NA
gene6	gene6_1	GATGGAGGGAGACGACTTGTCATCCTTGTCGCCATCACCGGTCCCGTACATTTTCTGTGGTGGGTTGAGGGGAAGGA	gene6	0	704	781	((759, ‘G’, ‘T’),)	()	GATGGAGGGAGACGACTTGTCATCCTTGTCGCCATCACCGGTCCCGTACATTTTCGGTGGTGGGTTGAGGGGAAGGA GATGGAGGGAGACGACTTGTCATCCTTGTCGCCATCACCGGTCCCGTACATTTTCTGTGGTGGGTTGAGGGGAAGGA	nan	False	False	-20:S:G-T	741	False	False	False	MDFPGGSGRRPQQQEPEHLPPMTPLPLARQGSVYSLTFDEFQSSLGGAAKDFGSMNMDELLRSIWSAEEVHSVAAASASAADHAHAAARGPVSIQHQGSLTLPRTLSQKTVDEVWRDLTCVGGGPSSGSAAPAAPPPPAQRHPTLGEITLEEFLVRAGVVREDMTAPPPVPPAPVCPAPAPRPPVLFPHGNVLAPLVPPLQFGNGFVSGAVGQQRGGPVPPAVSPRPVTASAFGKMEGDDLSSLSPSPVPYIFGGGLRGRKPPAMEKVVERRQRRMIKNRESAARSRQRKQKNPHGTGARLNGDGVAVTSVFGLDGEDHREGDQRRPKEAAEAHERSREARDVTRQKTGEYTDASREAAQEARDRSRATAQEGRHRRQGEGGQGRGRGHSSATRIWR*	100.0	False	NA	1.1	NA	3.4	NA	NA	NA	NA
gene6	gene6_1	GATGGAGGGAGACGACTTGTCATCCTTGTCGCCATCCGGTCCCGTACATTTTCGGTGGTGGGTTGAGGGGAAGGA	gene6	2	704	781	()	((739, ‘TCA’, ‘T’),)	GATGGAGGGAGACGACTTGTCATCCTTGTCGCCATCACCGGTCCCGTACATTTTCGGTGGTGGGTTGAGGGGAAGGA GATGGAGGGAGACGACTTGTCATCCTTGTCGCCAT–CCGGTCCCGTACATTTTCGGTGGTGGGTTGAGGGGAAGGA	True	nan	True	0:2D:TCA-T	741	False	False	False	MDFPGGSGRRPQQQEPEHLPPMTPLPLARQGSVYSLTFDEFQSSLGGAAKDFGSMNMDELLRSIWSAEEVHSVAAASASAADHAHAAARGPVSIQHQGSLTLPRTLSQKTVDEVWRDLTCVGGGPSSGSAAPAAPPPPAQRHPTLGEITLEEFLVRAGVVREDMTAPPPVPPAPVCPAPAPRPPVLFPHGNVLAPLVPPLQFGNGFVSGAVGQQRGGPVPPAVSPRPVTASAFGKMEGDDLSSLSPSGPVHFRWWVEGKEATGYGEGG*	65.8	True	NA	NA	47.4	96.6	NA	49.8	NA	NA
gene7	gene7_1	TTTGCTGACCGACGTCACGTGCTGCAGGGCGCGGGCCGTGGGCTGGCCGCCGGTCCGCGCGTACCGGCGCAACGCGCTGCGCGACG	gene7	ref	304	390	nan	nan	nan	nan	nan	nan	ref	339				MQQDLRNSERRNPEQAHPVMSASSTNSAASPAVSGLDYDDTALTLALPGSSAEPAADRKRAHADHDKPPSPKARAVGWPPVRAYRRNALRDEARLVKVAVDGAPYLRKVDLAAHDGYAALLRALHGMFASCLVAGAGADGAGRIDTAAEYMPTYEDKDGDWMLVGDVPFKMFVDSCKRIRLMKSSEAVNLSPRTSSRQ*	NA	False	100.0	100.0	41.8	53.1	49.2	51.1	44.0	44.4
gene7	gene7_1	TTTGCTGACCGACGTCACGTGCTGCAGGGCGCGGGACCGTGGGCTGGCCGCCGGTCCGCGCGTACCGGCGCAACGCGCTGCGCGACG	gene7	-1	304	390	()	((339, ‘G’, ‘GA’),)	TTTGCTGACCGACGTCACGTGCTGCAGGGCGCGGG-CCGTGGGCTGGCCGCCGGTCCGCGCGTACCGGCGCAACGCGCTGCGCGACG TTTGCTGACCGACGTCACGTGCTGCAGGGCGCGGGACCGTGGGCTGGCCGCCGGTCCGCGCGTACCGGCGCAACGCGCTGCGCGACG	True	nan	True	2:1I:G-GA	339	False	False	False	MQQDLRNSERRNPEQAHPVMSASSTNSAASPAVSGLDYDDTALTLALPGSSAEPAADRKRAHADHDKPPSPKARDRGLAAGPRVPAQRAARRGQAREGGRGRRAVPAEGGPRGARRVRGPAPRAPRHVRLLPRCRSRSRRGGADRHRRRVHAHLRGQGRRLDARRRRPLQDVRGLVQEDPPHEELRGRQPISEDIIPAVIVVGVDAICPTRLISPN*	49.0	True	NA	NA	58.2	46.9	50.8	48.9	1.4	55.6
gene7	gene7_1	TTTGCTGACCGACGTCACGTGCTGCAGGGCGCGGCCGTGGGCTGGCCGCCGGTCCGCGCGTACCGGCGCAACGCGCTGCGCGACG	gene7	1	304	390	()	((336, ‘CG’, ‘C’),)	TTTGCTGACCGACGTCACGTGCTGCAGGGCGCGGGCCGTGGGCTGGCCGCCGGTCCGCGCGTACCGGCGCAACGCGCTGCGCGACG TTTGCTGACCGACGTCACGTGCTGCAGGGCGC-GGCCGTGGGCTGGCCGCCGGTCCGCGCGTACCGGCGCAACGCGCTGCGCGACG	True	nan	True	-1:1D:CG-C	339	False	False	False	MQQDLRNSERRNPEQAHPVMSASSTNSAASPAVSGLDYDDTALTLALPGSSAEPAADRKRAHADHDKPPSPKARPWAGRRSARTGATRCATRPGS*	43.4	True	NA	NA	NA	NA	NA	NA	54.6	NA
gene8	gene8_1	GCTGAATATTTTTTTCTCTTTGGTTTGTTGCTGTTGTTGTTGTTGGCTGATGCAGGGCTTCAGGAAGATAGTGGCGGACAGGTGGGA	gene8	ref	1767	1854	nan	nan	nan	nan	nan	nan	ref	1825				MAFLVERCGEMVVSMESPHAKPVPAPFLTKTYQLVDDPCTDHIVSWGDDDTTFVVWRPPEFARDLLPNYFKHNNFSSFVRQLNTYGFRKIVADRWEFANEFFRKGAKHLLAEIHRRKSSQPLPTPMPPHQPYHHHLHHLHHHLSPFSPPPLAQPVPSYHHHHFQEEPIATATAPHGGAQAGAAGGGNNEGSGAGSRRGLSGRANHVAPVTSPSSAAHASLPSAAGGGAAASSCRLMELDPADSPSPPRRPEADDGTDTVKLFGVALQGKKKKRAHQEDGDDGNHEQGSSDV*	NA	False	100.0	98.4	55.0	65.5	54.6	52.5	63.6	51.5
gene8	gene8_1	GCTGAATATTTTTTTCTCTTTGGTTTGTTGCTGTTGTTGTTGTTGGCTGATGCAGGGCTTTCAGGAAGATAGTGGCGGACAGGTGGGA	gene8	-1	1767	1854	()	((1825, ‘C’, ‘CT’),)	GCTGAATATTTTTTTCTCTTTGGTTTGTTGCTGTTGTTGTTGTTGGCTGATGCAGGGC-TTCAGGAAGATAGTGGCGGACAGGTGGGA GCTGAATATTTTTTTCTCTTTGGTTTGTTGCTGTTGTTGTTGTTGGCTGATGCAGGGCTTTCAGGAAGATAGTGGCGGACAGGTGGGA	True	nan	True	2:1I:C-CT	1825	False	False	False	MAFLVERCGEMVVSMESPHAKPVPAPFLTKTYQLVDDPCTDHIVSWGDDDTTFVVWRPPEFARDLLPNYFKHNNFSSFVRQLNTYGFQEDSGGQVGVRQRVLQEGRQAPTRRDPPEEVVAAAADADAAAPALPPPPPPSPPPPQPVLPAAAGTAGAVVPPPPLPRRAHRHRHRAARRCSSRRRRWRQQ*	39.1	True	NA	1.6	45.0	34.5	45.4	47.5	36.4	48.5
gene9	gene9_1	GGCGGCAAGCGCCTCCGCCCCGTGCTGGCCATCGCCGCGTGCGAGCTCGTGGGCGGGACCGCGGCCGCGGCCGTCCCGGTGGCGTGC	gene9	ref	315	402	nan	nan	nan	nan	nan	nan	ref	339				MNKLASCFLQHGAPHTQIFKSYHVQRSPSLQLLENRSVSMTRHRAADRAARGTIIDVAVDSGTSFDFESYLSAKARAVHNALDLTLQGLRCPEVLSESMRYSVLAGGKRLRPVLAIAACELVGGTAAAAVPVACAVEMIHTASLIHDDMPCMDDDALRRGRPSNHVAFGEPTALLAGDALLALAFEHVARGSAGAGVPADRALRAVVELGSVAGVGGIAAGQVADMASEGAPSGSVSLAALEYIHVHKTARLVEAAAVSGAVVGGGGDGEVERVRRYAHFLGLLGQVVDDVLDVTGTSEQLGKTAGKDVAAGKATYPRLMGLKGARAYMGELLAKAEAELDGLDAAPTAPLRHLARGGDHIDVMVVVGYDWVGFGVGIG*	NA	False	100.0	100.0	49.3	55.0	53.7	54.2	29.6	38.5
gene9	gene9_1	GGCGGCAAGCGCCTCCGCCCCGTGACTGGCCATCGCCGCGTGCGAGCTCGTGGGCGGGACCGCGGCCGCGGCCGTCCCGGTGGCGTGC	gene9	-1	315	402	()	((339, ‘G’, ‘GA’),)	GGCGGCAAGCGCCTCCGCCCCGTG-CTGGCCATCGCCGCGTGCGAGCTCGTGGGCGGGACCGCGGCCGCGGCCGTCCCGGTGGCGTGC GGCGGCAAGCGCCTCCGCCCCGTGACTGGCCATCGCCGCGTGCGAGCTCGTGGGCGGGACCGCGGCCGCGGCCGTCCCGGTGGCGTGC	True	nan	True	-2:1I:G-GA	339	False	False	False	MNKLASCFLQHGAPHTQIFKSYHVQRSPSLQLLENRSVSMTRHRAADRAARGTIIDVAVDSGTSFDFESYLSAKARAVHNALDLTLQGLRCPEVLSESMRYSVLAGGKRLRPVTGHRRVRARGRDRGRGRPGGVRRRDDPHRVAHPRRHAVHGRRRAPPRPPLQPRRVRRAHGATRRRRAAGARFRARRPRQRGRRRPRGPRAPRRRGARERSWRRRHRRGAGRRHGERGSPLRLREPGRAGVHPCA*	38.9	True	NA	NA	NA	NA	NA	NA	5.6	8.9
gene9	gene9_1	GGCGGCAAGCGCCTCCGCCCCGTGCCTGGCCATCGCCGCGTGCGAGCTCGTGGGCGGGACCGCGGCCGCGGCCGTCCCGGTGGCGTGC	gene9	-1	315	402	()	((339, ‘G’, ‘GC’),)	GGCGGCAAGCGCCTCCGCCCCGTG-CTGGCCATCGCCGCGTGCGAGCTCGTGGGCGGGACCGCGGCCGCGGCCGTCCCGGTGGCGTGC GGCGGCAAGCGCCTCCGCCCCGTGCCTGGCCATCGCCGCGTGCGAGCTCGTGGGCGGGACCGCGGCCGCGGCCGTCCCGGTGGCGTGC	True	nan	True	-2:1I:G-GC	339	False	False	False	MNKLASCFLQHGAPHTQIFKSYHVQRSPSLQLLENRSVSMTRHRAADRAARGTIIDVAVDSGTSFDFESYLSAKARAVHNALDLTLQGLRCPEVLSESMRYSVLAGGKRLRPVPGHRRVRARGRDRGRGRPGGVRRRDDPHRVAHPRRHAVHGRRRAPPRPPLQPRRVRRAHGATRRRRAAGARFRARRPRQRGRRRPRGPRAPRRRGARERSWRRRHRRGAGRRHGERGSPLRLREPGRAGVHPCA*	38.9	True	NA	NA	NA	NA	NA	NA	1.2	3.0
gene9	gene9_1	GGCGGCAAGCGCCTCCGCCCCGTGTCTGGCCATCGCCGCGTGCGAGCTCGTGGGCGGGACCGCGGCCGCGGCCGTCCCGGTGGCGTGC	gene9	-1	315	402	()	((339, ‘G’, ‘GT’),)	GGCGGCAAGCGCCTCCGCCCCGTG-CTGGCCATCGCCGCGTGCGAGCTCGTGGGCGGGACCGCGGCCGCGGCCGTCCCGGTGGCGTGC GGCGGCAAGCGCCTCCGCCCCGTGTCTGGCCATCGCCGCGTGCGAGCTCGTGGGCGGGACCGCGGCCGCGGCCGTCCCGGTGGCGTGC	True	nan	True	-2:1I:G-GT	339	False	False	False	MNKLASCFLQHGAPHTQIFKSYHVQRSPSLQLLENRSVSMTRHRAADRAARGTIIDVAVDSGTSFDFESYLSAKARAVHNALDLTLQGLRCPEVLSESMRYSVLAGGKRLRPVSGHRRVRARGRDRGRGRPGGVRRRDDPHRVAHPRRHAVHGRRRAPPRPPLQPRRVRRAHGATRRRRAAGARFRARRPRQRGRRRPRGPRAPRRRGARERSWRRRHRRGAGRRHGERGSPLRLREPGRAGVHPCA*	38.9	True	NA	NA	50.7	45.0	NA	NA	56.5	1.1
gene9	gene9_1	GGCGGCAAGCGCCTCCGCCCCGTGTGGCCATCGCCGCGTGCGAGCTCGTGGGCGGGACCGCGGCCGCGGCCGTCCCGGTGGCGTGC	gene9	1	315	402	()	((339, ‘GC’, ‘G’),)	GGCGGCAAGCGCCTCCGCCCCGTGCTGGCCATCGCCGCGTGCGAGCTCGTGGGCGGGACCGCGGCCGCGGCCGTCCCGGTGGCGTGC GGCGGCAAGCGCCTCCGCCCCGTG-TGGCCATCGCCGCGTGCGAGCTCGTGGGCGGGACCGCGGCCGCGGCCGTCCCGGTGGCGTGC	True	nan	True	-2:1D:GC-G	339	False	False	False	MNKLASCFLQHGAPHTQIFKSYHVQRSPSLQLLENRSVSMTRHRAADRAARGTIIDVAVDSGTSFDFESYLSAKARAVHNALDLTLQGLRCPEVLSESMRYSVLAGGKRLRPVWPSPRASSWAGPRPRPSRWRAPSR*	34.0	True	NA	NA	NA	NA	46.3	NA	2.3	2.4
gene9	gene9_1	GGCGGCAAGCGCCTCCGCCCCGTGGGCCATCGCCGCGTGCGAGCTCGTGGGCGGGACCGCGGCCGCGGCCGTCCCGGTGGCGTGC	gene9	2	315	402	()	((339, ‘GCT’, ‘G’),)	GGCGGCAAGCGCCTCCGCCCCGTGCTGGCCATCGCCGCGTGCGAGCTCGTGGGCGGGACCGCGGCCGCGGCCGTCCCGGTGGCGTGC GGCGGCAAGCGCCTCCGCCCCGTG–GGCCATCGCCGCGTGCGAGCTCGTGGGCGGGACCGCGGCCGCGGCCGTCCCGGTGGCGTGC	True	nan	True	-2:2D:GCT-G	339	False	False	False	MNKLASCFLQHGAPHTQIFKSYHVQRSPSLQLLENRSVSMTRHRAADRAARGTIIDVAVDSGTSFDFESYLSAKARAVHNALDLTLQGLRCPEVLSESMRYSVLAGGKRLRPVGHRRVRARGRDRGRGRPGGVRRRDDPHRVAHPRRHAVHGRRRAPPRPPLQPRRVRRAHGATRRRRAAGARFRARRPRQRGRRRPRGPRAPRRRGARERSWRRRHRRGAGRRHGERGSPLRLREPGRAGVHPCA*	38.9	True	NA	NA	NA	NA	NA	45.8	2.5	1.9
gene9	gene9_1	GGCGGCAAGCGCCTCCGCCCCGTGTGCCATCGCCGCGTGCGAGCTCGTGGGCGGGACCGCGGCCGCGGCCGTCCCGGTGGCGTGC	gene9	2	315	402	()	((339, ‘GC’, ‘G’), (341, ‘TG’, ‘T’))	GGCGGCAAGCGCCTCCGCCCCGTGCTGGCCATCGCCGCGTGCGAGCTCGTGGGCGGGACCGCGGCCGCGGCCGTCCCGGTGGCGTGC GGCGGCAAGCGCCTCCGCCCCGTG-T-GCCATCGCCGCGTGCGAGCTCGTGGGCGGGACCGCGGCCGCGGCCGTCCCGGTGGCGTGC	True	nan	True	-2:1D:GC-G,-4:1D:TG-T	339	False	False	False	MNKLASCFLQHGAPHTQIFKSYHVQRSPSLQLLENRSVSMTRHRAADRAARGTIIDVAVDSGTSFDFESYLSAKARAVHNALDLTLQGLRCPEVLSESMRYSVLAGGKRLRPVCHRRVRARGRDRGRGRPGGVRRRDDPHRVAHPRRHAVHGRRRAPPRPPLQPRRVRRAHGATRRRRAAGARFRARRPRQRGRRRPRGPRAPRRRGARERSWRRRHRRGAGRRHGERGSPLRLREPGRAGVHPCA*	38.9	True	NA	NA	NA	NA	NA	NA	NA	42.1
gene9	gene9_1	GGCGGCAAGCGCCTCCGCCCCGTGGCCATCGCCGCGTGCGAGCTCGTGGGCGGGACCGCGGCCGCGGCCGTCCCGGTGGCGTGC	gene9	3	315	402	()	((337, ‘GTGC’, ‘G’),)	GGCGGCAAGCGCCTCCGCCCCGTGCTGGCCATCGCCGCGTGCGAGCTCGTGGGCGGGACCGCGGCCGCGGCCGTCCCGGTGGCGTGC GGCGGCAAGCGCCTCCGCCCCG—TGGCCATCGCCGCGTGCGAGCTCGTGGGCGGGACCGCGGCCGCGGCCGTCCCGGTGGCGTGC	True	nan	True	0:3D:GTGC-G	339	False	False	False	MNKLASCFLQHGAPHTQIFKSYHVQRSPSLQLLENRSVSMTRHRAADRAARGTIIDVAVDSGTSFDFESYLSAKARAVHNALDLTLQGLRCPEVLSESMRYSVLAGGKRLRPVAIAACELVGGTAAAAVPVACAVEMIHTASLIHDDMPCMDDDALRRGRPSNHVAFGEPTALLAGDALLALAFEHVARGSAGAGVPADRALRAVVELGSVAGVGGIAAGQVADMASEGAPSGSVSLAALEYIHVHKTARLVEAAAVSGAVVGGGGDGEVERVRRYAHFLGLLGQVVDDVLDVTGTSEQLGKTAGKDVAAGKATYPRLMGLKGARAYMGELLAKAEAELDGLDAAPTAPLRHLARGGDHIDVMVVVGYDWVGFGVGIG*	99.7	False	NA	NA	NA	NA	NA	NA	2.3	2.1

Haplotype	Reference	Locus	Target	Expected cut site	FILTER_gRNA	atgCheck	splicingSiteCheck	protein_sequence	pairwiseProteinIdentity (%)	Effect	sample1	sample2	sample3	sample4	sample5	sample6	sample7	sample8
gene1_1_ref	gene1	gene1_1	gene1	1817	False			MGSSYDPYPSPGADDLFLYLSDLGPASPSAYLDLPPTPQPQPYPQSQQQQQGSKGPTQDMLLPYISSMLMEDDIDDTFFYDYPDNPALLQAQQSFLDILSDDASSPTTTTGTTNSSASVNHSSSDASASAPPTPAAVDSYSPAPAVQFDGFDLDPAAFFSNGANSDLMSSAFLKGMEEANKFLPSQDKLVIDLDPPDDTKRFVLPTRAAENLAPGFNAAATTVPAAVAMAVKEEEVILAALDAALGSGGVVLGRGRRNRLDDDEEDLELQRRSTKQSALQGDGDERDVFEKYIMTCPETCTEQMQQLRIAMQEEAAKEAAVAAGNGKAKGRRGGREVVDLRTLLVHCAQAVASDDRRSATELLRQIKQHASPQGDATQRLAHCFAEGLQARLAGTGSMVYQSLMAKRTSAADILQAYQLYMAAICFKRVVFVFSNNTIYNAALGKMKIHIVDYGIHYGFQWPCFLRWIADREGGPPEVRITGIDLPQPGFRPTQRIEETGRRLSKYAQQFGVPFKYQAIAASKMESIRAEDLNLDPEEVLIVNCLYQFKNLMDESVVIESPRDIVLNNIRKMRPHTFIHAIVNGSFSAPFFVTRFREALFFYSALFDALDTTTPRDSNQRMLIEENLFGRAALNVIACEGTDRVERPETYKQWQVRNQRAGLKQQPLNPDVVQQDIGTSNQEEICDASMS*	NA	False	100.0	100.0	100.0	100.0	100.0	100.0	100.0	100.0
gene2_1_ref	gene2	gene2_1	gene2	3795	False			EFPCRWGRRRRHVSPRYRLGHTSVRVGGRHTLAAPACVCSPPTLPALALHFPWQSSLVPDFLPERIRPPSIRPPVPAGLRGSSAWDQDPSRPRHPRAKDRIKARTNILGMVADTESSDSLPGSSNAASEMPANGSIHRKSQEKPPKKTHKAEREKLKRDQLNDLFVELGSMLDLDRQNTGKATVLGDAARVLRDLITQVESLRQEQSALVSERQYVSSEKNELQEENSSLKSQISELQTELCARMRSSSLSQTSIGMSDPATHQQMQMWSSIPHLSSVAMAARPASAASPLHGQEGYSADAGQAGYAPQPQPRELQLFPGSSASSSPERERSSRLGSGQATPPSLTDSLPGQLCLSLLQPSQEASGGGGGGVMSRSREERRDG*	NA	False	100.0	100.0	48.2	NA	57.2	100.0	45.9	100.0
gene2_1_-1:2D:ACT-A	gene2	gene2_1	gene2	3795	True	False	False	EFPCRWGRRRRHVSPRYRLGHTSVRVGGRHTLAAPACVCSPPTLPALALHFPWQSSLVPDFLPERIRPPSIRPPVPAGLRGSSAWDQDPSRPRHPRAKDRIKARTNILGMVADTESSDSLPGSSNAASEMPANGSIHRKSQEKPPKKTHKAEREKLKRDQLNDLFVELGSMLDLDRQNTGKATVLGDAARVLRDLITSGISQAGTICSCIGAPICQFREE*	54.8	True	NA	NA	51.8	45.0	NA	NA	NA	NA
gene2_1_-1:3D:ACTC-A	gene2	gene2_1	gene2	3795	True	False	False	EFPCRWGRRRRHVSPRYRLGHTSVRVGGRHTLAAPACVCSPPTLPALALHFPWQSSLVPDFLPERIRPPSIRPPVPAGLRGSSAWDQDPSRPRHPRAKDRIKARTNILGMVADTESSDSLPGSSNAASEMPANGSIHRKSQEKPPKKTHKAEREKLKRDQLNDLFVELGSMLDLDRQNTGKATVLGDAARVLRDLIKVESLRQEQSALVSERQYVSSEKNELQEENSSLKSQISELQTELCARMRSSSLSQTSIGMSDPATHQQMQMWSSIPHLSSVAMAARPASAASPLHGQEGYSADAGQAGYAPQPQPRELQLFPGSSASSSPERERSSRLGSGQATPPSLTDSLPGQLCLSLLQPSQEASGGGGGGVMSRSREERRDG*	99.5	False	NA	NA	NA	55.0	42.8	NA	54.1	NA
gene3_1_ref	gene3	gene3_1	gene3	3121	False			MAMPFASLSPAADHRPSSLLPYCRAAPLSAVGEDAAAQAQQQQQHAMSGRWAARPPALFTAAQYEELEHQALIYKYLVAGVPVPPDLLLPLRRGFVYHQPALGYGPYFGKKVDPEPGRCRRTDGKKWRCSKEAAPDSKYCERHMHRGRNRSRKPVEAQLVPPPHAQQQQQQQAPAPTAGFQSHPMYPSILAGNGGGGGGVGGGAGGGGTFGLGPTSQLHMDSAAAYATAAGGGSKDLRYSAYGVKSLSDEHSQLLSGGGGMDASMDNSWRLLPSQTAATFQATSYPLFGALSGLDESTIASLPKTQREPLSFFGSDFVTPKQENQTLRPFFDEWPKSRDSWPELNEDNSLGSSATQLSISIPMAPSDFNTSSRSPNGIPSR*	NA	False	100.0	100.0	49.9	NA	52.4	NA	4.2	5.0
gene3_1_-1:1D:CG-C	gene3	gene3_1	gene3	3121	True	False	False	MAMPFASLSPAADHRPSSLLPYCRAAPLSAVGEDAAAQAQQQQQHAMSGRWAARPPALFTAAQYEELEHQALIYKYLVAGVPVPPDLLLPLRRGFVYHQPALGYGPYFGKKVDPEPGRCRRTDGKKWRCSKEAAPDSKYCERHMHRGRNRSRKPVEAQLVPPPHAQQQQQQQAPAPTAGFQSHPMYPSILAGNGGGGGGVGGGAGGGGTFGLGPTSQLHMDSAAAYATAAGGGSKDLRYSAYG*	63.8	True	NA	NA	NA	NA	NA	NA	24.6	25.0
gene3_1_-1:1I:C-CG	gene3	gene3_1	gene3	3121	True	False	False	MAMPFASLSPAADHRPSSLLPYCRAAPLSAVGEDAAAQAQQQQQHAMSGRWAARPPALFTAAQYEELEHQALIYKYLVAGVPVPPDLLLPLRRGFVYHQPALGYGPYFGKKVDPEPGRCRRTDGKKWRCSKEAAPDSKYCERHMHRGRNRSRKPVEAQLVPPPHAQQQQQQQAPAPTAGFQSHPMYPSILAGNGGGGGGVGGGAGGGGTFGLGPTSQLHMDSAAAYATAAGGGSKDLRYSAYGGEVSVGRAQPALVRRRRHGRVNGQLVAPVAVPNRRHVPGHKLPSVRRAERSGREHHRLAAQDAEGAPLLLRERLRDPEAGEPDAAPLLRRVAQVEGLVAGAERGQQPRLLGHPALHLHPHGALRLQHQLQIAEWNTVKVKPSIRRHTCFFFLLFFRFEPFVLRTFF*	62.6	True	NA	NA	47.9	55.5	47.6	40.3	47.5	56.0
gene3_1_-1:2D:CGG-C	gene3	gene3_1	gene3	3121	True	False	False	MAMPFASLSPAADHRPSSLLPYCRAAPLSAVGEDAAAQAQQQQQHAMSGRWAARPPALFTAAQYEELEHQALIYKYLVAGVPVPPDLLLPLRRGFVYHQPALGYGPYFGKKVDPEPGRCRRTDGKKWRCSKEAAPDSKYCERHMHRGRNRSRKPVEAQLVPPPHAQQQQQQQAPAPTAGFQSHPMYPSILAGNGGGGGGVGGGAGGGGTFGLGPTSQLHMDSAAAYATAAGGGSKDLRYSAYGEVSVGRAQPALVRRRRHGRVNGQLVAPVAVPNRRHVPGHKLPSVRRAERSGREHHRLAAQDAEGAPLLLRERLRDPEAGEPDAAPLLRRVAQVEGLVAGAERGQQPRLLGHPALHLHPHGALRLQHQLQIAEWNTVKVKPSIRRHTCFFFLLFFRFEPFVLRTFF*	62.5	True	NA	NA	2.2	NA	NA	59.7	4.2	2.0
gene3_1_-1:3D:CGGG-C	gene3	gene3_1	gene3	3121	True	False	False	MAMPFASLSPAADHRPSSLLPYCRAAPLSAVGEDAAAQAQQQQQHAMSGRWAARPPALFTAAQYEELEHQALIYKYLVAGVPVPPDLLLPLRRGFVYHQPALGYGPYFGKKVDPEPGRCRRTDGKKWRCSKEAAPDSKYCERHMHRGRNRSRKPVEAQLVPPPHAQQQQQQQAPAPTAGFQSHPMYPSILAGNGGGGGGVGGGAGGGGTFGLGPTSQLHMDSAAAYATAAGGGSKDLRYSAYVKSLSDEHSQLLSGGGGMDASMDNSWRLLPSQTAATFQATSYPLFGALSGLDESTIASLPKTQREPLSFFGSDFVTPKQENQTLRPFFDEWPKSRDSWPELNEDNSLGSSATQLSISIPMAPSDFNTSSRSPNGIPSR*	99.7	False	NA	NA	NA	NA	NA	NA	4.2	NA
gene3_1_-1:5D:CGGGGT-C	gene3	gene3_1	gene3	3121	True	False	False	MAMPFASLSPAADHRPSSLLPYCRAAPLSAVGEDAAAQAQQQQQHAMSGRWAARPPALFTAAQYEELEHQALIYKYLVAGVPVPPDLLLPLRRGFVYHQPALGYGPYFGKKVDPEPGRCRRTDGKKWRCSKEAAPDSKYCERHMHRGRNRSRKPVEAQLVPPPHAQQQQQQQAPAPTAGFQSHPMYPSILAGNGGGGGGVGGGAGGGGTFGLGPTSQLHMDSAAAYATAAGGGSKDLRYSAYEVSVGRAQPALVRRRRHGRVNGQLVAPVAVPNRRHVPGHKLPSVRRAERSGREHHRLAAQDAEGAPLLLRERLRDPEAGEPDAAPLLRRVAQVEGLVAGAERGQQPRLLGHPALHLHPHGALRLQHQLQIAEWNTVKVKPSIRRHTCFFFLLFFRFEPFVLRTFF*	62.6	True	NA	NA	NA	NA	NA	NA	1.7	NA
gene3_1_-1:S:G-T	gene3	gene3_1	gene3	3121	True	False	False	MAMPFASLSPAADHRPSSLLPYCRAAPLSAVGEDAAAQAQQQQQHAMSGRWAARPPALFTAAQYEELEHQALIYKYLVAGVPVPPDLLLPLRRGFVYHQPALGYGPYFGKKVDPEPGRCRRTDGKKWRCSKEAAPDSKYCERHMHRGRNRSRKPVEAQLVPPPHAQQQQQQQAPAPTAGFQSHPMYPSILAGNGGGGGGVGGGAGGGGTFGLGPTSQLHMDSAAAYATAAGGGSKDLRYSAYWVKSLSDEHSQLLSGGGGMDASMDNSWRLLPSQTAATFQATSYPLFGALSGLDESTIASLPKTQREPLSFFGSDFVTPKQENQTLRPFFDEWPKSRDSWPELNEDNSLGSSATQLSISIPMAPSDFNTSSRSPNGIPSR*	99.7	False	NA	NA	NA	NA	NA	NA	NA	3.0
gene3_1_-2:10D:GGGGTGAAGTC-G	gene3	gene3_1	gene3	3121	True	False	False	MAMPFASLSPAADHRPSSLLPYCRAAPLSAVGEDAAAQAQQQQQHAMSGRWAARPPALFTAAQYEELEHQALIYKYLVAGVPVPPDLLLPLRRGFVYHQPALGYGPYFGKKVDPEPGRCRRTDGKKWRCSKEAAPDSKYCERHMHRGRNRSRKPVEAQLVPPPHAQQQQQQQAPAPTAGFQSHPMYPSILAGNGGGGGGVGGGAGGGGTFGLGPTSQLHMDSAAAYATAAGGGSKDLRYSAYVCRTSTASSCPAAAAWTRQWTTRGACCRPKPPPRSRPQATLCSAR*	69.3	True	NA	NA	NA	NA	47.6	NA	NA	NA
gene3_1_-2:1I:G-GT	gene3	gene3_1	gene3	3121	True	False	False	MAMPFASLSPAADHRPSSLLPYCRAAPLSAVGEDAAAQAQQQQQHAMSGRWAARPPALFTAAQYEELEHQALIYKYLVAGVPVPPDLLLPLRRGFVYHQPALGYGPYFGKKVDPEPGRCRRTDGKKWRCSKEAAPDSKYCERHMHRGRNRSRKPVEAQLVPPPHAQQQQQQQAPAPTAGFQSHPMYPSILAGNGGGGGGVGGGAGGGGTFGLGPTSQLHMDSAAAYATAAGGGSKDLRYSAYVGEVSVGRAQPALVRRRRHGRVNGQLVAPVAVPNRRHVPGHKLPSVRRAERSGREHHRLAAQDAEGAPLLLRERLRDPEAGEPDAAPLLRRVAQVEGLVAGAERGQQPRLLGHPALHLHPHGALRLQHQLQIAEWNTVKVKPSIRRHTCFFFLLFFRFEPFVLRTFF*	63.1	True	NA	NA	NA	44.5	NA	NA	7.6	9.0
gene3_1_1:8D:TACGGGGTG-T	gene3	gene3_1	gene3	3121	True	False	False	MAMPFASLSPAADHRPSSLLPYCRAAPLSAVGEDAAAQAQQQQQHAMSGRWAARPPALFTAAQYEELEHQALIYKYLVAGVPVPPDLLLPLRRGFVYHQPALGYGPYFGKKVDPEPGRCRRTDGKKWRCSKEAAPDSKYCERHMHRGRNRSRKPVEAQLVPPPHAQQQQQQQAPAPTAGFQSHPMYPSILAGNGGGGGGVGGGAGGGGTFGLGPTSQLHMDSAAAYATAAGGGSKDLRYSA*	63.3	True	NA	NA	NA	NA	NA	NA	2.5	NA
gene3_1_34:28D:TGCTCACTTGCTGACATACCTAGGTACTC-T,3:8D:CCTACGGGG-C	gene3	gene3_1	gene3	3121	True	False	True	MAMPFASLSPAADHRPSSLLPYCRAAPLSAVGEDAAAQAQQQQQHAMSGRWAARPPALFTAAQYEELEHQALIYKYLVAGVPVPPDLLLPLRRGFVYHQPALGYGPYFGKKVDPEPGRCRRTDGKKWRCSKEAAPDSKYCERHMHRGRNRSRKPVEAQLVPPPHAQQQQQQQAPAPTAGFQSHPMYPSILAGNGGGGGGVGGGAGGGGTFGLGPTSQLHMDSAAAYATAAGGGSKDLX*	62.2	True	NA	NA	NA	NA	NA	NA	3.5	NA
gene4_1_ref	gene4	gene4_1	gene4	861	False			MEGGQDVFLGAAARAPPPPPSCPFHGSATATRSGGAQMLSFSSNGVAGLGLCSGASKMQGVLSRVRRPFTPTQWMELEHQALIYKHFAVNAPVPSSLLLPIKRSLNPWSSLGSSSLGWAPFRSGSADAEPGRCRRTDGKKWRCSRDAVGDQKYCERHIKRGCHRSRKHVEGRKATPTTADPTMAVSGGSLLHSHAVAWQQQGKSSAANVTDPFSLGSNRNLLDKQNLGDQFSISTSMDSFDFSSSHSSPNQAKVAFSPVAMQHEHDQLYLVHGAGSSAENVNKSQDGQLLVSRETIDDGPLGEVFKGKSCQSASADILTDHWTSTRDLRPPTGILQMSSSNTVPAENHTSNSSYLMARMANSQTVPTLH*	NA	False	100.0	100.0	48.3	64.8	100.0	100.0	53.6	41.9
gene4_1_1:1D:TG-T	gene4	gene4_1	gene4	861	True	False	False	MEGGQDVFLGAAARAPPPPPSCPFHGSATATRSGGAQMLSFSSNGVAGLGLSQVPARCRVCCRG*	16.5	True	NA	NA	NA	NA	NA	NA	NA	1.3
gene4_1_2:1I:G-GA	gene4	gene4_1	gene4	861	True	False	False	MEGGQDVFLGAAARAPPPPPSCPFHGSATATRSGGAQMLSFSSNGVAGLGL*	13.8	True	NA	NA	NA	NA	NA	NA	NA	1.5
gene4_1_2:1I:G-GT	gene4	gene4_1	gene4	861	True	False	False	MEGGQDVFLGAAARAPPPPPSCPFHGSATATRSGGAQMLSFSSNGVAGLGLCLRCQQDAGCVVEGEEALHSDAVDGAGAPGPDLQALRCECPCAVQLAPPYQKKPQSMEQPWLQLIGMGTISFRLC*	23.6	True	NA	NA	51.7	35.2	NA	NA	46.4	55.3
gene5_1_ref	gene5	gene5_1	gene5	1212	False			MSSSSSSSSAATVFPPSPQLPPPLLVENLPPLHQLTPPVAAAAAPASEQLCYVHCHFCDTVLVVSVPTSSLFKTVTVRCGHCSSLLTVNMRGLLFPGTPANTAAAAAAAPPPPPAAVTSTTATITTAPAPPPATSVNNNGQFHFIPHSLDLALPIPPHQSLLLDEISSAANPSLQLLEQHGLGGMIPSGRNAAALHPHPPQPQPPAAGKGAKEPSPRANSAINRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLMPDHQGPKKTSLLPQDHQRSDGGGLLKEGLYAAAANMGVAPY*	NA	False	100.0	100.0	38.3	45.4	43.7	42.8	4.5	2.2
gene5_1_-1:1D:AC-A	gene5	gene5_1	gene5	1212	True	False	False	MSSSSSSSSAATVFPPSPQLPPPLLVENLPPLHQLTPPVAAAAAPASEQLCYVHCHFCDTVLVVSVPTSSLFKTVTVRCGHCSSLLTVNMRGLLFPGTPANTAAAAAAAPPPPPAAVTSTTATITTAPAPPPATSVNNNGQFHFIPHSLDLALPIPPHNPSCWTRYPAPRTRACSCWSSTASAA*	53.9	True	NA	NA	2.1	NA	NA	NA	12.3	18.5
gene5_1_-1:21D:ACCAATCCCTCCTGCTGGTAAG-A	gene5	gene5_1	gene5	1212	True	False	True	MSSSSSSSSAATVFPPSPQLPPPLLVENLPPLHQLTPPVAAAAAPASEQLCYVHCHFCDTVLVVSVPTSSLFKTVTVRCGHCSSLLTVNMRGLLFPGTPANTAAAAAAAPPPPPAAVTSTTATITTAPAPPPATSVNNNGQFHFIPHSLDLALPIPPX*	49.2	True	NA	NA	59.6	NA	56.3	57.2	71.2	NA
gene5_1_-1:5D:ACCAAT-A	gene5	gene5_1	gene5	1212	True	False	False	MSSSSSSSSAATVFPPSPQLPPPLLVENLPPLHQLTPPVAAAAAPASEQLCYVHCHFCDTVLVVSVPTSSLFKTVTVRCGHCSSLLTVNMRGLLFPGTPANTAAAAAAAPPPPPAAVTSTTATITTAPAPPPATSVNNNGQFHFIPHSLDLALPIPPHPPAGRDIQRREPEPAVAGAARPRRHDPQRQERGRAAPAPAPAPAARSG*	57.1	True	NA	NA	NA	NA	NA	NA	1.2	1.2
gene5_1_-2:1I:C-CA	gene5	gene5_1	gene5	1212	True	False	False	MSSSSSSSSAATVFPPSPQLPPPLLVENLPPLHQLTPPVAAAAAPASEQLCYVHCHFCDTVLVVSVPTSSLFKTVTVRCGHCSSLLTVNMRGLLFPGTPANTAAAAAAAPPPPPAAVTSTTATITTAPAPPPATSVNNNGQFHFIPHSLDLALPIPPHTIPPAGRDIQRREPEPAVAGAARPRRHDPQRQERGRAAPAPAPAPAARSG*	57.4	True	NA	NA	NA	NA	NA	NA	NA	1.7
gene5_1_-2:1I:C-CT	gene5	gene5_1	gene5	1212	True	False	False	MSSSSSSSSAATVFPPSPQLPPPLLVENLPPLHQLTPPVAAAAAPASEQLCYVHCHFCDTVLVVSVPTSSLFKTVTVRCGHCSSLLTVNMRGLLFPGTPANTAAAAAAAPPPPPAAVTSTTATITTAPAPPPATSVNNNGQFHFIPHSLDLALPIPPHSIPPAGRDIQRREPEPAVAGAARPRRHDPQRQERGRAAPAPAPAPAARSG*	57.4	True	NA	NA	NA	NA	NA	NA	1.2	3.0
gene5_1_-2:2D:CCA-C	gene5	gene5_1	gene5	1212	True	False	False	MSSSSSSSSAATVFPPSPQLPPPLLVENLPPLHQLTPPVAAAAAPASEQLCYVHCHFCDTVLVVSVPTSSLFKTVTVRCGHCSSLLTVNMRGLLFPGTPANTAAAAAAAPPPPPAAVTSTTATITTAPAPPPATSVNNNGQFHFIPHSLDLALPIPPHIPPAGRDIQRREPEPAVAGAARPRRHDPQRQERGRAAPAPAPAPAARSG*	57.4	True	NA	NA	NA	NA	NA	NA	6.0	4.3
gene5_1_-2:3D:CCAA-C	gene5	gene5_1	gene5	1212	True	False	False	MSSSSSSSSAATVFPPSPQLPPPLLVENLPPLHQLTPPVAAAAAPASEQLCYVHCHFCDTVLVVSVPTSSLFKTVTVRCGHCSSLLTVNMRGLLFPGTPANTAAAAAAAPPPPPAAVTSTTATITTAPAPPPATSVNNNGQFHFIPHSLDLALPIPPHSLLLDEISSAANPSLQLLEQHGLGGMIPSGRNAAALHPHPPQPQPPAAGKGAKEPSPRANSAINRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLMPDHQGPKKTSLLPQDHQRSDGGGLLKEGLYAAAANMGVAPY*	99.7	False	NA	NA	NA	54.6	NA	NA	1.9	2.3
gene5_1_-2:4D:CCAAT-C	gene5	gene5_1	gene5	1212	True	False	False	MSSSSSSSSAATVFPPSPQLPPPLLVENLPPLHQLTPPVAAAAAPASEQLCYVHCHFCDTVLVVSVPTSSLFKTVTVRCGHCSSLLTVNMRGLLFPGTPANTAAAAAAAPPPPPAAVTSTTATITTAPAPPPATSVNNNGQFHFIPHSLDLALPIPPHPSCWTRYPAPRTRACSCWSSTASAA*	53.6	True	NA	NA	NA	NA	NA	NA	NA	21.3
gene5_1_2:3D:CCCA-C	gene5	gene5_1	gene5	1212	True	False	False	MSSSSSSSSAATVFPPSPQLPPPLLVENLPPLHQLTPPVAAAAAPASEQLCYVHCHFCDTVLVVSVPTSSLFKTVTVRCGHCSSLLTVNMRGLLFPGTPANTAAAAAAAPPPPPAAVTSTTATITTAPAPPPATSVNNNGQFHFIPHSLDLALPIPPQSLLLDEISSAANPSLQLLEQHGLGGMIPSGRNAAALHPHPPQPQPPAAGKGAKEPSPRANSAINRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLMPDHQGPKKTSLLPQDHQRSDGGGLLKEGLYAAAANMGVAPY*	99.7	False	NA	NA	NA	NA	NA	NA	1.7	45.5
gene6_1_ref	gene6	gene6_1	gene6	741	False			MDFPGGSGRRPQQQEPEHLPPMTPLPLARQGSVYSLTFDEFQSSLGGAAKDFGSMNMDELLRSIWSAEEVHSVAAASASAADHAHAAARGPVSIQHQGSLTLPRTLSQKTVDEVWRDLTCVGGGPSSGSAAPAAPPPPAQRHPTLGEITLEEFLVRAGVVREDMTAPPPVPPAPVCPAPAPRPPVLFPHGNVLAPLVPPLQFGNGFVSGAVGQQRGGPVPPAVSPRPVTASAFGKMEGDDLSSLSPSPVPYIFGGGLRGRKPPAMEKVVERRQRRMIKNRESAARSRQRKQKNPHGTGARLNGDGVAVTSVFGLDGEDHREGDQRRPKEAAEAHERSREARDVTRQKTGEYTDASREAAQEARDRSRATAQEGRHRRQGEGGQGRGRGHSSATRIWR*	NA	False	100.0	97.8	52.6	3.4	100.0	50.2	100.0	100.0
gene6_1_-10:S:G-A	gene6	gene6_1	gene6	741	True	False	False	MDFPGGSGRRPQQQEPEHLPPMTPLPLARQGSVYSLTFDEFQSSLGGAAKDFGSMNMDELLRSIWSAEEVHSVAAASASAADHAHAAARGPVSIQHQGSLTLPRTLSQKTVDEVWRDLTCVGGGPSSGSAAPAAPPPPAQRHPTLGEITLEEFLVRAGVVREDMTAPPPVPPAPVCPAPAPRPPVLFPHGNVLAPLVPPLQFGNGFVSGAVGQQRGGPVPPAVSPRPVTASAFGKMEGDDLSSLSPSPVPYIFGGGLRGRKPPAMEKVVERRQRRMIKNRESAARSRQRKQKNPHGTGARLNGDGVAVTSVFGLDGEDHREGDQRRPKEAAEAHERSREARDVTRQKTGEYTDASREAAQEARDRSRATAQEGRHRRQGEGGQGRGRGHSSATRIWR*	100.0	False	NA	1.1	NA	NA	NA	NA	NA	NA
gene6_1_-6:S:T-C	gene6	gene6_1	gene6	741	True	False	False	MDFPGGSGRRPQQQEPEHLPPMTPLPLARQGSVYSLTFDEFQSSLGGAAKDFGSMNMDELLRSIWSAEEVHSVAAASASAADHAHAAARGPVSIQHQGSLTLPRTLSQKTVDEVWRDLTCVGGGPSSGSAAPAAPPPPAQRHPTLGEITLEEFLVRAGVVREDMTAPPPVPPAPVCPAPAPRPPVLFPHGNVLAPLVPPLQFGNGFVSGAVGQQRGGPVPPAVSPRPVTASAFGKMEGDDLSSLSPSPAPYIFGGGLRGRKPPAMEKVVERRQRRMIKNRESAARSRQRKQKNPHGTGARLNGDGVAVTSVFGLDGEDHREGDQRRPKEAAEAHERSREARDVTRQKTGEYTDASREAAQEARDRSRATAQEGRHRRQGEGGQGRGRGHSSATRIWR*	99.7	False	NA	1.1	NA	NA	NA	NA	NA	NA
gene6_1_0:2D:TCA-T	gene6	gene6_1	gene6	741	True	False	False	MDFPGGSGRRPQQQEPEHLPPMTPLPLARQGSVYSLTFDEFQSSLGGAAKDFGSMNMDELLRSIWSAEEVHSVAAASASAADHAHAAARGPVSIQHQGSLTLPRTLSQKTVDEVWRDLTCVGGGPSSGSAAPAAPPPPAQRHPTLGEITLEEFLVRAGVVREDMTAPPPVPPAPVCPAPAPRPPVLFPHGNVLAPLVPPLQFGNGFVSGAVGQQRGGPVPPAVSPRPVTASAFGKMEGDDLSSLSPSGPVHFRWWVEGKEATGYGEGG*	65.8	True	NA	NA	47.4	96.6	NA	49.8	NA	NA
gene7_1_ref	gene7	gene7_1	gene7	339	False			MQQDLRNSERRNPEQAHPVMSASSTNSAASPAVSGLDYDDTALTLALPGSSAEPAADRKRAHADHDKPPSPKARAVGWPPVRAYRRNALRDEARLVKVAVDGAPYLRKVDLAAHDGYAALLRALHGMFASCLVAGAGADGAGRIDTAAEYMPTYEDKDGDWMLVGDVPFKMFVDSCKRIRLMKSSEAVNLSPRTSSRQ*	NA	False	100.0	100.0	41.8	53.1	49.2	51.1	44.0	44.4
gene7_1_-1:1D:CG-C	gene7	gene7_1	gene7	339	True	False	False	MQQDLRNSERRNPEQAHPVMSASSTNSAASPAVSGLDYDDTALTLALPGSSAEPAADRKRAHADHDKPPSPKARPWAGRRSARTGATRCATRPGS*	43.4	True	NA	NA	NA	NA	NA	NA	54.6	NA
gene7_1_2:1I:G-GA	gene7	gene7_1	gene7	339	True	False	False	MQQDLRNSERRNPEQAHPVMSASSTNSAASPAVSGLDYDDTALTLALPGSSAEPAADRKRAHADHDKPPSPKARDRGLAAGPRVPAQRAARRGQAREGGRGRRAVPAEGGPRGARRVRGPAPRAPRHVRLLPRCRSRSRRGGADRHRRRVHAHLRGQGRRLDARRRRPLQDVRGLVQEDPPHEELRGRQPISEDIIPAVIVVGVDAICPTRLISPN*	49.0	True	NA	NA	58.2	46.9	50.8	48.9	1.4	55.6
gene8_1_ref	gene8	gene8_1	gene8	1825	False			MAFLVERCGEMVVSMESPHAKPVPAPFLTKTYQLVDDPCTDHIVSWGDDDTTFVVWRPPEFARDLLPNYFKHNNFSSFVRQLNTYGFRKIVADRWEFANEFFRKGAKHLLAEIHRRKSSQPLPTPMPPHQPYHHHLHHLHHHLSPFSPPPLAQPVPSYHHHHFQEEPIATATAPHGGAQAGAAGGGNNEGSGAGSRRGLSGRANHVAPVTSPSSAAHASLPSAAGGGAAASSCRLMELDPADSPSPPRRPEADDGTDTVKLFGVALQGKKKKRAHQEDGDDGNHEQGSSDV*	NA	False	100.0	98.4	55.0	65.5	54.6	52.5	63.6	51.5
gene8_1_2:1I:C-CT	gene8	gene8_1	gene8	1825	True	False	False	MAFLVERCGEMVVSMESPHAKPVPAPFLTKTYQLVDDPCTDHIVSWGDDDTTFVVWRPPEFARDLLPNYFKHNNFSSFVRQLNTYGFQEDSGGQVGVRQRVLQEGRQAPTRRDPPEEVVAAAADADAAAPALPPPPPPSPPPPQPVLPAAAGTAGAVVPPPPLPRRAHRHRHRAARRCSSRRRRWRQQ*	39.1	True	NA	1.6	45.0	34.5	45.4	47.5	36.4	48.5
gene9_1_ref	gene9	gene9_1	gene9	339	False			MNKLASCFLQHGAPHTQIFKSYHVQRSPSLQLLENRSVSMTRHRAADRAARGTIIDVAVDSGTSFDFESYLSAKARAVHNALDLTLQGLRCPEVLSESMRYSVLAGGKRLRPVLAIAACELVGGTAAAAVPVACAVEMIHTASLIHDDMPCMDDDALRRGRPSNHVAFGEPTALLAGDALLALAFEHVARGSAGAGVPADRALRAVVELGSVAGVGGIAAGQVADMASEGAPSGSVSLAALEYIHVHKTARLVEAAAVSGAVVGGGGDGEVERVRRYAHFLGLLGQVVDDVLDVTGTSEQLGKTAGKDVAAGKATYPRLMGLKGARAYMGELLAKAEAELDGLDAAPTAPLRHLARGGDHIDVMVVVGYDWVGFGVGIG*	NA	False	100.0	100.0	49.3	55.0	53.7	54.2	29.6	38.5
gene9_1_-2:1D:GC-G	gene9	gene9_1	gene9	339	True	False	False	MNKLASCFLQHGAPHTQIFKSYHVQRSPSLQLLENRSVSMTRHRAADRAARGTIIDVAVDSGTSFDFESYLSAKARAVHNALDLTLQGLRCPEVLSESMRYSVLAGGKRLRPVWPSPRASSWAGPRPRPSRWRAPSR*	34.0	True	NA	NA	NA	NA	46.3	NA	2.3	2.4
gene9_1_-2:1D:GC-G,-4:1D:TG-T	gene9	gene9_1	gene9	339	True	False	False	MNKLASCFLQHGAPHTQIFKSYHVQRSPSLQLLENRSVSMTRHRAADRAARGTIIDVAVDSGTSFDFESYLSAKARAVHNALDLTLQGLRCPEVLSESMRYSVLAGGKRLRPVCHRRVRARGRDRGRGRPGGVRRRDDPHRVAHPRRHAVHGRRRAPPRPPLQPRRVRRAHGATRRRRAAGARFRARRPRQRGRRRPRGPRAPRRRGARERSWRRRHRRGAGRRHGERGSPLRLREPGRAGVHPCA*	38.9	True	NA	NA	NA	NA	NA	NA	NA	42.1
gene9_1_-2:1I:G-GA	gene9	gene9_1	gene9	339	True	False	False	MNKLASCFLQHGAPHTQIFKSYHVQRSPSLQLLENRSVSMTRHRAADRAARGTIIDVAVDSGTSFDFESYLSAKARAVHNALDLTLQGLRCPEVLSESMRYSVLAGGKRLRPVTGHRRVRARGRDRGRGRPGGVRRRDDPHRVAHPRRHAVHGRRRAPPRPPLQPRRVRRAHGATRRRRAAGARFRARRPRQRGRRRPRGPRAPRRRGARERSWRRRHRRGAGRRHGERGSPLRLREPGRAGVHPCA*	38.9	True	NA	NA	NA	NA	NA	NA	5.6	8.9
gene9_1_-2:1I:G-GC	gene9	gene9_1	gene9	339	True	False	False	MNKLASCFLQHGAPHTQIFKSYHVQRSPSLQLLENRSVSMTRHRAADRAARGTIIDVAVDSGTSFDFESYLSAKARAVHNALDLTLQGLRCPEVLSESMRYSVLAGGKRLRPVPGHRRVRARGRDRGRGRPGGVRRRDDPHRVAHPRRHAVHGRRRAPPRPPLQPRRVRRAHGATRRRRAAGARFRARRPRQRGRRRPRGPRAPRRRGARERSWRRRHRRGAGRRHGERGSPLRLREPGRAGVHPCA*	38.9	True	NA	NA	NA	NA	NA	NA	1.2	3.0
gene9_1_-2:1I:G-GT	gene9	gene9_1	gene9	339	True	False	False	MNKLASCFLQHGAPHTQIFKSYHVQRSPSLQLLENRSVSMTRHRAADRAARGTIIDVAVDSGTSFDFESYLSAKARAVHNALDLTLQGLRCPEVLSESMRYSVLAGGKRLRPVSGHRRVRARGRDRGRGRPGGVRRRDDPHRVAHPRRHAVHGRRRAPPRPPLQPRRVRRAHGATRRRRAAGARFRARRPRQRGRRRPRGPRAPRRRGARERSWRRRHRRGAGRRHGERGSPLRLREPGRAGVHPCA*	38.9	True	NA	NA	50.7	45.0	NA	NA	56.5	1.1
gene9_1_-2:2D:GCT-G	gene9	gene9_1	gene9	339	True	False	False	MNKLASCFLQHGAPHTQIFKSYHVQRSPSLQLLENRSVSMTRHRAADRAARGTIIDVAVDSGTSFDFESYLSAKARAVHNALDLTLQGLRCPEVLSESMRYSVLAGGKRLRPVGHRRVRARGRDRGRGRPGGVRRRDDPHRVAHPRRHAVHGRRRAPPRPPLQPRRVRRAHGATRRRRAAGARFRARRPRQRGRRRPRGPRAPRRRGARERSWRRRHRRGAGRRHGERGSPLRLREPGRAGVHPCA*	38.9	True	NA	NA	NA	NA	NA	45.8	2.5	1.9
gene9_1_0:3D:GTGC-G	gene9	gene9_1	gene9	339	True	False	False	MNKLASCFLQHGAPHTQIFKSYHVQRSPSLQLLENRSVSMTRHRAADRAARGTIIDVAVDSGTSFDFESYLSAKARAVHNALDLTLQGLRCPEVLSESMRYSVLAGGKRLRPVAIAACELVGGTAAAAVPVACAVEMIHTASLIHDDMPCMDDDALRRGRPSNHVAFGEPTALLAGDALLALAFEHVARGSAGAGVPADRALRAVVELGSVAGVGGIAAGQVADMASEGAPSGSVSLAALEYIHVHKTARLVEAAAVSGAVVGGGGDGEVERVRRYAHFLGLLGQVVDDVLDVTGTSEQLGKTAGKDVAAGKATYPRLMGLKGARAYMGELLAKAEAELDGLDAAPTAPLRHLARGGDHIDVMVVVGYDWVGFGVGIG*	99.7	False	NA	NA	NA	NA	NA	NA	2.3	2.1

Reference	Locus	SNP	INDEL	Haplotype_Name	sample2	sample3	sample4	sample5	sample6	sample7	sample8
gene1	gene1_1	()	()	nan	0.0	0.0	0.0	0.0	0.0	0.0	0.0
gene2	gene2_1	nan	(3792, ‘ACT’, ‘A’)	-1:2D:ACT-A	0.0	51.8	45.0	0.0	0.0	0.0	0.0
gene3	gene3_1	(3145, ‘A’, ‘C’)	(3120, ‘C’, ‘CG’),(3121, ‘G’, ‘GT’),(3120, ‘CG’, ‘C’),(3120, ‘CG’, ‘C’),(3120, ‘CGG’, ‘C’),(3120, ‘CGGGGT’, ‘C’),(3118, ‘TACGGGGTG’, ‘T’),(3121, ‘GGGGTGAAGTC’, ‘G’),(3085, ‘TGCTCACTTGCTGACATACCTAGGTACTC’, ‘T’),(3116, ‘CCTACGGGG’, ‘C’)	-1:1I:C-CG,-2:1I:G-GT,-1:1D:CG-C,-1:1D:CG-C,-26:S:A-C,-1:2D:CGG-C,-1:5D:CGGGGT-C,1:8D:TACGGGGTG-T,-2:10D:GGGGTGAAGTC-G,34:28D:TGCTCACTTGCTGACATACCTAGGTACTC-T,3:8D:CCTACGGGG-C	0.0	50.1	100.0	95.2	100.0	91.60000000000001	92.0
gene4	gene4_1	nan	(861, ‘G’, ‘GA’),(861, ‘G’, ‘GT’),(860, ‘TG’, ‘T’)	2:1I:G-GA,2:1I:G-GT,1:1D:TG-T	0.0	51.7	35.2	0.0	0.0	46.4	58.099999999999994
gene5	gene5_1	nan	(1212, ‘C’, ‘CA’),(1212, ‘C’, ‘CT’),(1211, ‘AC’, ‘A’),(1212, ‘CCA’, ‘C’),(1212, ‘CCAAT’, ‘C’),(1211, ‘ACCAAT’, ‘A’),(1211, ‘ACCAATCCCTCCTGCTGGTAAG’, ‘A’)	-2:1I:C-CA,-2:1I:C-CT,-1:1D:AC-A,-2:2D:CCA-C,-2:4D:CCAAT-C,-1:5D:ACCAAT-A,-1:21D:ACCAATCCCTCCTGCTGGTAAG-A	0.0	61.7	0.0	56.3	57.2	91.9	50.0
gene6	gene6_1	nan	(739, ‘TCA’, ‘T’)	0:2D:TCA-T	0.0	47.4	96.6	0.0	49.8	0.0	0.0
gene7	gene7_1	nan	(339, ‘G’, ‘GA’),(336, ‘CG’, ‘C’)	2:1I:G-GA,-1:1D:CG-C	0.0	58.2	46.9	50.8	48.9	56.0	55.6
gene8	gene8_1	nan	(1825, ‘C’, ‘CT’)	2:1I:C-CT	1.6	45.0	34.5	45.4	47.5	36.4	48.5
gene9	gene9_1	nan	(339, ‘G’, ‘GA’),(339, ‘G’, ‘GC’),(339, ‘G’, ‘GT’),(339, ‘GC’, ‘G’),(339, ‘GCT’, ‘G’),(339, ‘GC’, ‘G’),(341, ‘TG’, ‘T’)	-2:1I:G-GA,-2:1I:G-GC,-2:1I:G-GT,-2:1D:GC-G,-2:2D:GCT-G,-2:1D:GC-G,-4:1D:TG-T	0.0	50.7	45.0	46.3	45.8	68.1	59.400000000000006

Reference	Locus	SNP	INDEL	Haplotype_Name	sample3	sample4	sample5	sample6	sample7	sample8
gene1	gene1_1	()	()	nan	0	0	0	0	0	0
gene2	gene2_1	nan	(3792, ‘ACT’, ‘A’)	-1:2D:ACT-A	1	1	0	0	0	0
gene3	gene3_1	(3145, ‘A’, ‘C’)	(3120, ‘C’, ‘CG’),(3121, ‘G’, ‘GT’),(3120, ‘CG’, ‘C’),(3120, ‘CG’, ‘C’),(3120, ‘CGG’, ‘C’),(3120, ‘CGGGGT’, ‘C’),(3118, ‘TACGGGGTG’, ‘T’),(3121, ‘GGGGTGAAGTC’, ‘G’),(3085, ‘TGCTCACTTGCTGACATACCTAGGTACTC’, ‘T’),(3116, ‘CCTACGGGG’, ‘C’)	-1:1I:C-CG,-2:1I:G-GT,-1:1D:CG-C,-1:1D:CG-C,-26:S:A-C,-1:2D:CGG-C,-1:5D:CGGGGT-C,1:8D:TACGGGGTG-T,-2:10D:GGGGTGAAGTC-G,34:28D:TGCTCACTTGCTGACATACCTAGGTACTC-T,3:8D:CCTACGGGG-C	1	2	2	2	2	2
gene4	gene4_1	nan	(861, ‘G’, ‘GA’),(861, ‘G’, ‘GT’),(860, ‘TG’, ‘T’)	2:1I:G-GA,2:1I:G-GT,1:1D:TG-T	1	1	0	0	1	1
gene5	gene5_1	nan	(1212, ‘C’, ‘CA’),(1212, ‘C’, ‘CT’),(1211, ‘AC’, ‘A’),(1212, ‘CCA’, ‘C’),(1212, ‘CCAAT’, ‘C’),(1211, ‘ACCAAT’, ‘A’),(1211, ‘ACCAATCCCTCCTGCTGGTAAG’, ‘A’)	-2:1I:C-CA,-2:1I:C-CT,-1:1D:AC-A,-2:2D:CCA-C,-2:4D:CCAAT-C,-1:5D:ACCAAT-A,-1:21D:ACCAATCCCTCCTGCTGGTAAG-A	1	0	1	1	2	1
gene6	gene6_1	nan	(739, ‘TCA’, ‘T’)	0:2D:TCA-T	1	2	0	1	0	0
gene7	gene7_1	nan	(339, ‘G’, ‘GA’),(336, ‘CG’, ‘C’)	2:1I:G-GA,-1:1D:CG-C	1	1	1	1	1	1
gene8	gene8_1	nan	(1825, ‘C’, ‘CT’)	2:1I:C-CT	1	1	1	1	1	1
gene9	gene9_1	nan	(339, ‘G’, ‘GA’),(339, ‘G’, ‘GC’),(339, ‘G’, ‘GT’),(339, ‘GC’, ‘G’),(339, ‘GCT’, ‘G’),(339, ‘GC’, ‘G’),(341, ‘TG’, ‘T’)	-2:1I:G-GA,-2:1I:G-GC,-2:1I:G-GT,-2:1D:GC-G,-2:2D:GCT-G,-2:1D:GC-G,-4:1D:TG-T	1	1	1	1	1	1