Mercurial > repos > john-mccallum > pcr_markers
changeset 5:b321e0517be3 draft
Uploaded
| author | ben-warren |
|---|---|
| date | Thu, 22 May 2014 20:30:19 -0400 |
| parents | be070a68521e |
| children | f201e8c6e004 |
| files | CAPS2gff.sh Galaxy-Workflow-CAPS_Marker_Design_from_VCF.ga Galaxy-Workflow-CAPS_Marker_Development_from_454_Read_Mapping.ga README.md design_primers.py design_primers.xml find_CAPS.xml gsmapper2gff.sh ipcress.xml ipcress_gff.xml parse_primersearch.pl run_p3.py test-data/find_caps_output.txt test-data/freebayes_out.vcf test-data/freebayes_vcf_to_gff_output.gff test-data/ipcress.out test-data/ipcress_gff.out test-data/ipcress_test_input.txt test-data/mpileup_out.vcf test-data/mpileup_vcf_to_gff_output.gff test-data/targets test-data/targets.fasta test-data/targets.gff umelt_service.py uniq.xml vcf2gvf.py vcf2gvf.sh vcf2gvf.xml vcf_gff.py vcf_gff.xml |
| diffstat | 30 files changed, 2875 insertions(+), 774 deletions(-) [+] |
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--- a/CAPS2gff.sh Thu Oct 18 19:47:07 2012 -0400 +++ b/CAPS2gff.sh Thu May 22 20:30:19 2014 -0400 @@ -1,5 +1,7 @@ #!/bin/sh ##convert output of CAPS detection tool to GFF3 +## usage +# sh CAPS2gff.sh <input tabular CAPS output> <output file> #Copyright 2012 John McCallum #New Zealand Institute for Plant and Food Research
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Thu May 22 20:30:19 2014 -0400 @@ -0,0 +1,24 @@ +galaxy-pcr-markers +================== + +Scripts for design of PCR-based Marker Assays from DNA sequence variant data, and xml wrappers for use in Galaxy workflow environment + +Also available for download at Galaxy Toolshed http://toolshed.g2.bx.psu.edu/ +hg clone http://toolshed.g2.bx.psu.edu/repos/john-mccallum/pcr_markers + +NOTE that the primer design tool *design_primers.py* relies on EMBOSS ePrimer3 which depends on Primer3 1.1.4. +The updated tool *design_HRM_primers.py* does not have this restriction and should work with Primer3 V2. + +Please see development branch HRM for optimised design of high-resolution melting PCR assays using the uMelt web service at University of Utah. + + +**CITATION** +A Toolkit For Bulk PCR-Based Marker Design From Next-Generation Sequence Data: Application For Development Of A Framework Linkage Map In Bulb Onion (Allium cepa L.) (2012) + +Samantha Baldwin, Roopashree Revanna, Susan Thomson, Meeghan Pither-Joyce, Kathryn Wright, Ross Crowhurst, Mark Fiers, Leshi Chen, Richard MacKnight, John A. McCallum + +BMC Genomics 2012, 13:637 http://www.biomedcentral.com/1471-2164/13/637/abstract + +**Acknowledgements** +Current development of these tools is funded by the New Zealand Ministry for Business, Innovation & Employment project 'Virtual Institute of Statistical Genetics' (VISG) +See http://www.visg.co.nz
--- a/design_primers.py Thu Oct 18 19:47:07 2012 -0400 +++ b/design_primers.py Thu May 22 20:30:19 2014 -0400 @@ -1,9 +1,13 @@ -#!/usr/local/bin/python2.6 -##design primers to features in multiple sequences -##usage: python design_primers.py <fasta-file> <gff file> <file of target IDs> <prod_min_size> <prod_max_size> +#!/usr/bin/env python +##design primers to features in multiple sequences, with option to predict melting +#usage: design_HRM_primers.py [-h] -i IN_FILE -g GFF_FILE -T TARGET_FILE [-u] +# [-n MAX_PRIMERS] [-p PROD_MIN_SIZE] +# [-P PROD_MAX_SIZE] [-l OPT_PRIMER_LENGTH] +# [-m MAX_TM_DIFF] [-t OPTIMUM_TM] +# [-G OPT_GC_PERCENT] [-x MAXPOLYX] [-c GC_CLAMP] -#Copyright 2012 John McCallum & Leshi Chen +#Copyright 2013 John McCallum & Susan Thomson #New Zealand Institute for Plant and Food Research #This program is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -18,44 +22,86 @@ # You should have received a copy of the GNU General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. - import os import StringIO import re -import tempfile -import subprocess import copy import sys from BCBio import GFF from BCBio.GFF import GFFExaminer from Bio import SeqIO -from Bio.Emboss.Applications import Primer3Commandline -from Bio.Emboss import Primer3 +import run_p3 as P3 +#import umelt_service as umelts +import argparse + +##Primer3 defaults or additional options defined as dictionary +def_dict={ +'PRIMER_MIN_SIZE':'18', +'PRIMER_MAX_SIZE':'25', +'PRIMER_MAX_NS_ACCEPTED':'1'} + +#parse arguments +parser = argparse.ArgumentParser(description='Primer set design and melt prediction parameters') +parser.add_argument('-i', type=argparse.FileType('r'), help="input sequence file, required", dest='in_file', required=True) +parser.add_argument('-g', type=argparse.FileType('r'), help="input gff file with SNP and indels, required", dest='gff_file', required=True) +parser.add_argument('-T', type=argparse.FileType('r'), help="input target SNP file, required", dest='target_file', required=True) +parser.add_argument('-u',help="do uMelt prediction, optional", dest='run_uMelt',action='store_true', default=False ) +parser.add_argument('-n', type=int, help="maximum number of primer pairs to return, default=5", dest='max_primers', default=5) ## PRIMER_NUM_RETURN +parser.add_argument('-p', type=int, help="minimum product size", dest='prod_min_size', default=100) ## PRIMER_PRODUCT_SIZE_RANGE min +parser.add_argument('-P', type=int, help="maximum product size", dest='prod_max_size', default=300) ## PRIMER_PRODUCT_SIZE_RANGE max +parser.add_argument('-l', type=int, help="optimum primer length", dest='opt_primer_length', default=20) ## PRIMER_OPT_SIZE +parser.add_argument('-m', type=int, help="maximum tm difference between primers", dest='max_tm_diff', default=1) ## PRIMER_PAIR_MAX_DIFF_TM +parser.add_argument('-t', type=int, help="optimum Tm for primers, recommend range 59 to 61", dest='optimum_tm', default=59) ## PRIMER_OPT_TM +parser.add_argument('-G', type=int, help="optimum GC percentage of primers", dest='opt_GC_percent', default=50) ## PRIMER_OPT_GC_PERCENT +parser.add_argument('-x', type=int, help="maximum polyx, recommend less than 4", dest='maxpolyx', default=3) ## PRIMER_MAX_POLY_X +parser.add_argument('-c', type=int, help="number of C/Gs at end, recommend 2", dest='gc_clamp', default=1) ## PRIMER_GC_CLAMP + +parser.add_argument('-e', type=int, help="maximum allowable 3'-anchored complementarity", dest='maxselfend', default=3) ## PRIMER_MAX_SELF_END +parser.add_argument('-a', type=int, help="maximum complementarity between left and right or self", dest='maxselfany', default=8) ## PRIMER_MAX_SELF_ANY +parser.add_argument('-maxgc', type=float, help="Maximum allowable percentage of Gs and Cs in any primer.", dest='maxgc', default=80.0) ## PRIMER_MAX_GC +parser.add_argument('-mingc', type=float, help="Minimum allowable percentage of Gs and Cs in any primer.", dest='mingc', default=20.0) ## PRIMER_MIN_GC -in_file = sys.argv[1] -gff_file = sys.argv[2] -target_file = sys.argv[3] -prod_min_size = int(sys.argv[4]) -prod_max_size = int(sys.argv[5]) +parser.add_argument('-d', type=str, help="variant indentifier delimiter, used to separate sequence ID from rest ", dest='target_delim', default=':') +try: + my_args = parser.parse_args() +except SystemExit: + print("\nOops, an argument is missing/invalid, exiting...\n") + sys.exit(0) + +##update from args. NEEDS TO BE FINISHED +productsizerange = str(my_args.prod_min_size) + "-" + str(my_args.prod_max_size) +def_dict['PRIMER_PRODUCT_SIZE_RANGE']=productsizerange +def_dict['PRIMER_NUM_RETURN']=str(my_args.max_primers +1) +def_dict['PRIMER_OPT_SIZE']=str(my_args.opt_primer_length) +def_dict['PRIMER_PAIR_MAX_DIFF_TM']=str(my_args.max_tm_diff) +def_dict['PRIMER_OPT_TM']=str(my_args.optimum_tm) +def_dict['PRIMER_OPT_GC_PERCENT']=str(my_args.opt_GC_percent) +def_dict['PRIMER_MAX_POLY_X']=str(my_args.maxpolyx) +def_dict['PRIMER_GC_CLAMP']=str(my_args.gc_clamp) -max_tm_diff=1 ## -opt_GC_percent=50 ## -maxpolyx=4 ## -optimum_length=20 -##target is specified in start, end format -productsizerange = str(prod_min_size) + "," + str(prod_max_size) +def_dict['PRIMER_MAX_SELF_END']=str(my_args.maxselfend) +def_dict['PRIMER_MAX_SELF_ANY']=str(my_args.maxselfany) +def_dict['PRIMER_MAX_GC']=str(my_args.maxgc) +def_dict['PRIMER_MIN_GC']=str(my_args.mingc) + + + +##conditional import of umelt +if my_args.run_uMelt: + import umelt_service as umelts + #open input files -in_seq_handle = open(in_file) -in_gff_handle = open(gff_file) -in_target_handle=open(target_file) -#read target feature IDs into list -targets=in_target_handle.readlines() -in_target_handle.close() + +targets=my_args.target_file.readlines() +my_args.target_file.close() ##and create a hit list of sequences from this -target_seq_id_list = list(set([line.split(":")[0] for line in targets])) +target_seq_id_list = [re.split(my_args.target_delim,X)[0] for X in targets] ## target_delimiter defaults to ':' e.g. ABC:SNP:SAMTOOL:1234 + +##print header +print "SNP_Target_ID", "Position","Ref_base","Variant_base" ,"Amplicon_bp","PRIMER_LEFT_SEQUENCE",'PRIMER_RIGHT_SEQUENCE', "ref_melt_Tm","var_melt_Tm","Tm_difference" ##create iterator returning sequence records -for myrec in SeqIO.parse(in_seq_handle, "fasta"): +for myrec in SeqIO.parse(my_args.in_file, "fasta"): #check if this sequence is included in the target list if myrec.id in target_seq_id_list: ##create sequence dictionary so we can add in gff annotations @@ -63,9 +109,9 @@ ##just limit to gff annotations for this sequence limit_info = dict(gff_id = [ myrec.id ]) ##rewind gff filehandle - in_gff_handle.seek(0) + my_args.gff_file.seek(0) ##read annotations into sequence dictionary for this sequence record only - annotations = [r for r in GFF.parse(in_gff_handle, base_dict=seq_dict,limit_info=limit_info)] + annotations = [r for r in GFF.parse(my_args.gff_file, base_dict=seq_dict,limit_info=limit_info)] ##if there are any annotations, then proceed. if annotations: rec=annotations[0] @@ -75,79 +121,58 @@ target_annotations = [f for f in rec.features if f.id == target_ID ] if target_annotations: mytarget = target_annotations[0] - #create temporary files - tempfastaFile = tempfile.mktemp() - tempproutfile = tempfile.mktemp() #just consider slice of sequence in a window of +/- prod_max_size bp ##from feature UNLESS feature is close to end ##Note that slice is zero-based featLocation = mytarget.location.start.position - if featLocation > prod_max_size: - slice_start = featLocation - prod_max_size - featPosition = prod_max_size + if featLocation > my_args.prod_max_size: + slice_start = featLocation - my_args.prod_max_size + featPosition = my_args.prod_max_size else: slice_start = 0 featPosition = featLocation - if (len(rec) - featLocation) < prod_max_size: + if (len(rec) - featLocation) < my_args.prod_max_size: slice_end = len(rec) else: - slice_end = featLocation + prod_max_size + slice_end = featLocation + my_args.prod_max_size ###grab slice of sequence fom this window. targetRec = rec[slice_start:slice_end] matching_feature = [f for f in targetRec.features if f.id == mytarget.id] if matching_feature: target_feat = matching_feature[0] + my_target_dict={} # re-initialize target dictionary if target_feat.location.start.position == 0: target_feat.location.start.position = 1 - #we get the mask features by removing the target...all features are masked as just using snp and indels - ##a smarter filter could be added - ##note use of list copy to avoid possible side-effects - exclude_feat = list(targetRec.features) + #get the mask features by removing target...all features are masked as just using snp and indels, a smarter filter could be added + exclude_feat = list(targetRec.features) ##list copy to avoid possible side-effects exclude_feat.remove(target_feat) - ##print'targetRec.features', targetRec.features ##for debug - mask_str=map(lambda f: str(f.location.start.position+1) + "," + str(f.location.end.position + 1) ,exclude_feat) - #mask_str=map(lambda f: str(f.location).strip('[]'),exclude_feat) - p3_exclude_str = str(mask_str).replace('\', \'',':') - p3_target = str(target_feat.location.start.position +1) + "," + str(target_feat.location.end.position +1) - #write sequence record into template file as fasta - t_output_handle = open(tempfastaFile, "w") - SeqIO.write([targetRec], t_output_handle, "fasta") - t_output_handle.close() - #create Primer3Commandline() for emboss tool - primer_cl = Primer3Commandline() - #set the emboss tool to suppress output as this will make Galaxy think it is error message although it is a message to state run success - primer_cl.set_parameter("-auto",'1') - #pass sequence file to emboss - primer_cl.set_parameter("-sequence",tempfastaFile) - #add target location - primer_cl.set_parameter("-target", p3_target) - ##mask off other features...dumb masking of everything at present, beware - if (p3_exclude_str != ""): - primer_cl.set_parameter("-excludedregion", p3_exclude_str) - #add temporary output file to get the result - primer_cl.set_parameter("-outfile", tempproutfile) - #specify maximum different of tm - primer_cl.set_parameter("-maxdifftm",max_tm_diff ) - #other useful parameters - primer_cl.set_parameter("-ogcpercent", opt_GC_percent) - primer_cl.set_parameter("-opolyxmax", maxpolyx) - primer_cl.set_parameter("-osize", optimum_length) - #set product size range - primer_cl.set_parameter("-prange", productsizerange) - #using python subprocess method to run emboss command line programe with the parameters given - fnull = open(os.devnull, 'w') - result=subprocess.check_call(str(primer_cl),shell=True ,stdout = fnull, stderr = fnull) - #read temporary outputfile - handle = open(tempproutfile) - record = Primer3.read(handle) - ##just return first set, if there is one - if len(record.primers) > 0: - primer= record.primers[0] - outputstr=[mytarget.id, primer.forward_seq,primer.reverse_seq,primer.size] - else: - outputstr=[mytarget.id,"NONE","NONE","NONE"] - print('\t'.join(map(str,outputstr))) + excludes_str=' '.join([str(x.location.start.position)+','+str(x.location.end.position -x.location.start.position) for x in exclude_feat]) + my_target_dict={'SEQUENCE_ID' : rec.name, 'SEQUENCE_TEMPLATE': targetRec.seq.tostring(),'SEQUENCE_TARGET': str(target_feat.location.start.position) + ',1','SEQUENCE_INTERNAL_EXCLUDED_REGION': excludes_str} + my_target_dict.update(def_dict) ##add in defaults + result=P3.run_P3(target_dict=my_target_dict) + if my_args.run_uMelt: + amp_seq=targetRec.seq ##need to make this conditional on getting a result >0 and melt=True + mutamp_seq=targetRec.seq.tomutable() + mutamp_seq[target_feat.location.start:target_feat.location.end]=target_feat.qualifiers['Variant_seq'][0] #mutate to variant + for primerset in result: + amp_start=int(primerset['PRIMER_LEFT'].split(',')[0]) + amp_end=int(primerset['PRIMER_RIGHT'].split(',')[0]) + ref_melt_Tm=0 + var_melt_Tm=0 + if my_args.run_uMelt: + try: + ref_melt_Tm=umelts.getTm(umelts.getmelt(amp_seq.tostring()[amp_start:amp_end+1])) + var_melt_Tm=umelts.getTm(umelts.getmelt(mutamp_seq.tostring()[amp_start:amp_end+1])) + except: + ref_melt_Tm=0 ##preferably something more informative? + var_melt_Tm=0 ##exception handling to be added + reference_seq=target_feat.qualifiers['Reference_seq'][0] + if target_feat.qualifiers.has_key('Variant_seq'): + variant_seq=target_feat.qualifiers['Variant_seq'][0] + else: + variant_seq="NA" + print mytarget.id, featLocation + 1 ,reference_seq, variant_seq,amp_end-amp_start,primerset['PRIMER_LEFT_SEQUENCE'],primerset['PRIMER_RIGHT_SEQUENCE'], ref_melt_Tm,var_melt_Tm,abs(ref_melt_Tm-var_melt_Tm)#, amp_seq.tostring()[amp_start:amp_end+1], mutamp_seq.tostring()[amp_start:amp_end+1] - -in_gff_handle.close() -in_seq_handle.close() +my_args.gff_file.close() +my_args.in_file.close() +
--- a/design_primers.xml Thu Oct 18 19:47:07 2012 -0400 +++ b/design_primers.xml Thu May 22 20:30:19 2014 -0400 @@ -1,14 +1,25 @@ <?xml version="1.0"?> <tool id="Genetic_Marker_Design_2" name="Design primers to features"> <description>Design PCR Primers to Features</description> - <command interpreter="python">design_primers.py $inputfastaFile $inputSNPfile $inputTargetfile $min_size $max_size > $primer_outputfile </command> + <command interpreter="python -W ignore"> + #if 'Yes' in $uMelt.value + design_primers.py -i $inputfastaFile -g $inputSNPfile -T $inputTargetfile -p $min_size -P $max_size -u > $primer_outputfile + #else + design_primers.py -i $inputfastaFile -g $inputSNPfile -T $inputTargetfile -p $min_size -P $max_size > $primer_outputfile + #end if + </command> + <inputs> <param format="fasta" name="inputfastaFile" type="data" label="Multifasta Source file" /> <param format="gff3" name="inputSNPfile" type="data" label="annotation file(Gff3)" /> <param format="txt" name="inputTargetfile" type="data" optional="false" label="Target file" help="IN FORMAT Sequence id:source:type:start e.g. 1174806:gsMapper:SNP:292" ></param> <param name="min_size" size="20" type="text" value="75" label="Minimum Product Size Range" /> <param name="max_size" size="20" type="text" value="100" label="Maximum Product Size Range" /> - </inputs> + <param name="uMelt" type="select" label="uMelt prediction for HRM"> + <option value="No" selected= "true">No</option> + <option value="Yes">Yes</option> + </param> + </inputs> <outputs> <data format="tabular" name="primer_outputfile" /> </outputs> @@ -18,6 +29,7 @@ **TIP** This tool designs primer pairs to flank features +Optionally it can predict reference and variant Tm using the uMelt web service provided by University of Utah It takes
--- a/find_CAPS.xml Thu Oct 18 19:47:07 2012 -0400 +++ b/find_CAPS.xml Thu May 22 20:30:19 2014 -0400 @@ -9,6 +9,13 @@ <outputs> <data format="interval" name="outputfile" /> </outputs> + <tests> + <test> + <param name="inputSNPGff3File" value="targets.gff" ftype="gff3"/> + <param name="inputFasta" value="targets.fasta" ftype="fasta"/> + <output name="outputfile" file="find_caps_output.txt"/> + </test> + </tests> <help> .. class:: infomark @@ -32,7 +39,7 @@ -*input GFF* +*input GFF3* ::
--- a/gsmapper2gff.sh Thu Oct 18 19:47:07 2012 -0400 +++ b/gsmapper2gff.sh Thu May 22 20:30:19 2014 -0400 @@ -15,6 +15,8 @@ # You should have received a copy of the GNU General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. +##usage gsmapper2gff.sh <input 454HCDiffs.txt or 454AllDiffs.txt file> <output gff3 file> + infile=$1 outfile=$2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ipcress.xml Thu May 22 20:30:19 2014 -0400 @@ -0,0 +1,56 @@ +<?xml version="1.0"?> +<tool id="ipcress" name="In-Silico PCR Experiment Simulation System"> + <description>In-Silico PCR Experiment Simulation System</description> + <version_command>ipcress -v</version_command> + <command> + awk -v min=$min_length -v max=$max_length '{print $1,$2,$3, min, max}' $input_primers | ipcress -i /dev/stdin -s $input_seqs -m $mismatch $products_as_fasta $pretty -S $seed_length > $pcr_products + </command> + <inputs> + <param format="txt" name="input_primers" type="data" label="PCR Experiment Data" /> + <param format="fasta" name="input_seqs" type="data" label="Sequences (Fasta)" /> + <param name="mismatch" size="10" type="integer" value="0" label="Mismatches allowed per primer" /> + <param name="min_length" size="10" type="integer" value="50" label="Minimum PCR product length" /> + <param name="max_length" size="10" type="integer" value="100" label="Maximum PCR product length" /> + <param name="products_as_fasta" type="boolean" truevalue="-P" falsevalue="" label="Display PCR products as a FASTA format sequence" /> + <param name="pretty" type="boolean" truevalue="-p 1" falsevalue="-p 0" checked="true" label="Display Result in pretty format" /> + <param name="seed_length" size="10" type="integer" value="12" label="Seed length: 0 => Use Full Primer Length" /> + </inputs> + <outputs> + <data format="txt" name="pcr_products" /> + </outputs> + <stdio> + <exit_code range="1:" level="fatal" description="Fatal Error" /> + </stdio> + <tests> + <test> + <param name="input_primers" value="ipcress_test_input.txt" ftype="txt" /> + <param name="input_seqs" value="targets.fasta" ftype="fasta" /> + <output name="pcr_products" file="ipcress.out" /> + </test> + </tests> + <help> +ipcress is the In-silico PCR Experiment Simulation System. + +This is a tool for simulation of PCR experiments. You supply a file containing primers and a set of sequences, and it predicts PCR products. + +INPUT FORMAT + +The input for ipcress is a simple white-space delimited file describing +one experiment per line. Each line contains the following 5 fields: + +id An identifier for this experiment +primer_A Sequence for the first primer +primer_B Sequence for the second primer +min_product_len Minimum product length to report +max_product_len Maximum product length to report + +Here is an example line in this format: + +ID0001 CATGCATGCATGC CGATGCANGCATGCT 900 1100 + +MANUAL + +https://www.ebi.ac.uk/~guy/exonerate/ipcress.man.html + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ipcress_gff.xml Thu May 22 20:30:19 2014 -0400 @@ -0,0 +1,22 @@ +<?xml version="1.0"?> +<tool id="ipcress_gff" name="IPCRESS to GFF"> + <description>Convert output from In-Silico PCR Experiment Simulation System to GFF format</description> + <command> + awk '/^ipcress:/, split($2,HIT,":"){print HIT[1],$3,$4,$5,$6,$7,$8,$9,$10,$11}' $input1 | awk -v OFS='\t' '{print $1,"ipcress","PCR_product",$5,$8,".","+",".","Name="$2}' > $output1 + </command> + <inputs> + <param format="txt" name="input1" type="data" label="iPCRESS ouptut" /> + </inputs> + <outputs> + <data format="gff" name="output1" /> + </outputs> + <tests> + <test> + <param name="input1" value="ipcress.out" ftype="txt" /> + <output name="output1" file="ipcress_gff.out" /> + </test> + </tests> + <help> +Uses awk to parse IPCRESS output to gff file format + </help> +</tool>
--- a/parse_primersearch.pl Thu Oct 18 19:47:07 2012 -0400 +++ b/parse_primersearch.pl Thu May 22 20:30:19 2014 -0400 @@ -1,7 +1,7 @@ #!/usr/bin/perl #parse_primersearch.pl #reformat EMBOSS primersearch output into columnar Galaxy interval format - +#usage perl parse_primersearch.pl <input primersearch file> <tabular output file> #Copyright 2012 John McCallum #New Zealand Institute for Plant and Food Research #This program is free software: you can redistribute it and/or modify @@ -20,7 +20,7 @@ open (IN, "<$ARGV[0]"); open (OUT, ">$ARGV[1]"); -#print OUT "primerset_id","\t","sequence_id","\t","hit_start","\","mismatches","\t","amplimer_size",\n"; +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/run_p3.py Thu May 22 20:30:19 2014 -0400 @@ -0,0 +1,49 @@ +#!/usr/bin/pyrthon +##run primer3 by passing Python dictionary + +#un_P3.py + +import subprocess as sp +import copy + + +if "check_output" not in dir(sp): # duck punch it in! + def f(*popenargs, **kwargs): + if 'stdout' in kwargs: + raise ValueError('stdout argument not allowed, it will be overridden.') + process = sp.Popen(stdout=sp.PIPE, *popenargs, **kwargs) + output, unused_err = process.communicate() + retcode = process.poll() + if retcode: + cmd = kwargs.get("args") + if cmd is None: + cmd = popenargs[0] + raise sp.CalledProcessError(retcode,cmd) + return output + sp.check_output = f + + + + +##call P3 with dict of args, returns dict, no exception handling +def run_P3(target_dict): + p3_str='' + for key in target_dict: + p3_str+=key + p3_str+='=' + p3_str+=str(target_dict[key]) + p3_str+='\n' + p3_str+='=' + input_str='echo -e \"' + p3_str + '\" | primer3_core ' +###exception handling to be added here + output = sp.check_output(input_str,shell=True) + output_fields=output.split('\n') + ##put output into a dict, omitting trailing = + P3_dict=dict([X.split('=') for X in output_fields][:len(output_fields)-2]) + ##return iterable list + primer_list=[dict(PRIMER_RIGHT_SEQUENCE=P3_dict.get('PRIMER_RIGHT_'+ str(X) + '_SEQUENCE'),PRIMER_LEFT=P3_dict.get('PRIMER_LEFT_'+ str(X) ),PRIMER_RIGHT=P3_dict.get('PRIMER_RIGHT_'+ str(X) ),PRIMER_LEFT_SEQUENCE=P3_dict.get('PRIMER_LEFT_'+ str(X) + '_SEQUENCE')) for X in range(0,int(P3_dict.get('PRIMER_RIGHT_NUM_RETURNED'))-1)] + return(primer_list) + + + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/find_caps_output.txt Thu May 22 20:30:19 2014 -0400 @@ -0,0 +1,1 @@ +k69_93535 1147 1149 k69_93535:SAMTOOLS:SNP:1147 TaqI variant
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/freebayes_out.vcf Thu May 22 20:30:19 2014 -0400 @@ -0,0 +1,500 @@ +##fileformat=VCFv4.1 +##fileDate=20140410 +##source=freeBayes version 0.9.6 +##reference=localref.fa +##phasing=none +##commandline="freebayes --bam localbam_0.bam --fasta-reference localref.fa --vcf /data/galaxy/galaxy-dist/database/files/000/dataset_31.dat" +##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus"> +##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes"> +##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> +##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]"> +##INFO=<ID=RO,Number=1,Type=Integer,Description="Reference allele observations"> +##INFO=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations"> +##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous"> +##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome"> +##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio. Ratio between depth in samples with each called alternate allele and those without."> +##INFO=<ID=XRM,Number=1,Type=Float,Description="Reference allele read mismatch rate: The rate of SNPs + MNPs + INDELs in reads supporting the reference allele."> +##INFO=<ID=XRS,Number=1,Type=Float,Description="Reference allele read SNP rate: The rate of per-base mismatches (SNPs + MNPs) in reads supporting the reference allele."> +##INFO=<ID=XRI,Number=1,Type=Float,Description="Reference allele read INDEL rate: The rate of INDELs (gaps) in reads supporting the reference allele."> +##INFO=<ID=XAM,Number=A,Type=Float,Description="Alternate allele read mismatch rate: The rate of SNPs + MNPs + INDELs in reads supporting the alternate allele, excluding the called variant."> +##INFO=<ID=XAS,Number=A,Type=Float,Description="Alternate allele read SNP rate: The rate of per-base mismatches (SNPs + MNPs) in reads supporting the alternate allele, excluding the called variant."> +##INFO=<ID=XAI,Number=A,Type=Float,Description="Alternate allele read INDEL rate: The rate of INDELs (gaps) in reads supporting the alternate allele, excluding the called variant."> +##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best."> +##INFO=<ID=BVAR,Number=0,Type=Flag,Description="The best genotype combination in the posterior is variant (non homozygous)."> +##INFO=<ID=CpG,Number=0,Type=Flag,Description="CpG site (either CpG, TpG or CpA)"> +##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex."> +##INFO=<ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing. Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR."> +##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position."> +##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles."> +##INFO=<ID=HWE,Number=1,Type=Float,Description="Phred-scaled discrete HWE prior probability of the genotyping across all samples."> +##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length"> +##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles"> +##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles"> +##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments"> +##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype"> +##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy"> +##FORMAT=<ID=GLE,Number=1,Type=String,Description="Genotype Likelihood Explicit, same as GL, but with tags to indicate the specific genotype. For instance, 0^-75.22|1^-223.42|0/0^-323.03|1/0^-99.29|1/1^-802.53 represents both haploid and diploid genotype likilehoods in a biallelic context"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> +##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count"> +##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations"> +##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count"> +##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT unknown +Chr1 106 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 200 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 217 . G T 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 249 . T A 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0.02;XRS=0.02;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 586 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 669 . T G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 682 . T G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 1007 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0103093;XAM=0.0309278;XAS=0.0206186;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 1012 . TGT AGA 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X1M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=3;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0.0309278;XAS=0.0309278;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 1056 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0103093;XAM=0.0309278;XAS=0.0206186;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 1067 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0103093;XAM=0.0309278;XAS=0.0206186;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 1257 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 1305 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 1319 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 1330 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 1441 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0105263;XAM=0.0421053;XAS=0.0315789;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 1451 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0105263;XAM=0.0421053;XAS=0.0315789;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 1460 . CTCTG ATCTC 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X3M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=5;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0.0421053;XAS=0.0421053;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 1480 . G C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0105263;XAM=0.0421053;XAS=0.0315789;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 1525 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0105263;XAM=0.0421053;XAS=0.0315789;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 1670 . G T 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0.02;XRS=0.02;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 1673 . T G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.03;XRS=0.03;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 1700 . GC TG 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=2X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=2;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=mnp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.02;XRS=0.02;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 1711 . T G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.03;XRS=0.03;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 2117 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 2154 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 2485 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0103093;XAM=0.0103093;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 2490 . AAA CAC 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X1M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=3;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0.0103093;XAS=0.0103093;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 2906 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 2925 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 3371 . CCCTT GCCTA 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X3M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=5;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0.0105263;XAS=0.0105263;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 3389 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0105263;XAM=0.0105263;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 3431 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 3464 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 3746 . C CT 46.0861 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1M1I;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=ins;XAI=0;XAM=0.0204082;XAS=0.0204082;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:17.0704:1:0:0:1:46:-4.6,-0.30103,0 +Chr1 3766 . C A 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0.0102041;XAM=0.0204082;XAS=0.0102041;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 3790 . T G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0.0102041;XAM=0.0204082;XAS=0.0102041;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 3855 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 5718 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 5754 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 5782 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 5792 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 6194 . G C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 6212 . G A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 6265 . G C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 6482 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 6515 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 6520 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 6534 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 6602 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 6853 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 7015 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 7406 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.04;XAS=0.04;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 7422 . G C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.04;XAS=0.04;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 7452 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.04;XAS=0.04;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 7460 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.04;XAS=0.04;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 7476 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.04;XAS=0.04;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 7843 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 7906 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 8214 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 8262 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 8279 . G T 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.04;XRS=0.04;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 8285 . C G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.04;XRS=0.04;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 8288 . G C 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.04;XRS=0.04;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 8298 . G C 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.04;XRS=0.04;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 8305 . G C 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.04;XRS=0.04;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 8329 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 8509 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 8547 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 8633 . G C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 8657 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 8894 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 8958 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 8968 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 9070 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 9100 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 9488 . G C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0104167;XAM=0.0208333;XAS=0.0104167;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 9514 . GTTT CTTG 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X2M1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=4;MEANALT=1;MQM=42;MQMR=34;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=complex;XAI=0;XAM=0.0208333;XAS=0.0208333;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 9532 . A T 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=34;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0.0104167;XAM=0.0208333;XAS=0.0104167;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 10064 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 10072 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 10082 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 10099 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 10499 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 11126 . C G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=6;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.02;XRS=0.02;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 11134 . A C 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=6;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.02;XRS=0.02;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 11141 . C G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=6;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.02;XRS=0.02;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 11159 . C G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=6;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.02;XRS=0.02;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 11169 . A C 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=6;MQMR=40;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.04;XRS=0.04;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 11208 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=6;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 11418 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 11547 . A T 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 11567 . C A 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0.02;XRS=0.02;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 11582 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 13312 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=11;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 13336 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=11;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 13352 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=11;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 13652 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 13666 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 13728 . T G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0.02;XRS=0.02;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 14087 . ATGAAA GTGAGC 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X3M2X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=6;MEANALT=1;MQM=0;MQMR=18;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=1;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=complex;XAI=0.0365854;XAM=0.097561;XAS=0.0609756;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 14103 . AGT GGC 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X1M1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=3;MEANALT=1;MQM=0;MQMR=18;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=1;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=complex;XAI=0.0365854;XAM=0.097561;XAS=0.0609756;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 14119 . A T 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=18;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=1;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0.0487805;XAM=0.097561;XAS=0.0487805;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 14126 . A G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=18;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=1;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0.0487805;XAM=0.097561;XAS=0.0487805;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 14131 . GGAGTG TGGGTT 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X1M1X2M1X;DP=3;DPRA=0;EPP=5.18177;EPPR=7.35324;HWE=-0;LEN=6;MEANALT=1;MQM=0;MQMR=9;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=1;PAIREDR=0;RO=2;RPP=5.18177;RPPR=3.0103;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=complex;XAI=0.0365854;XAM=0.097561;XAS=0.0609756;XRI=0;XRM=0.025;XRS=0.025 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23 +Chr1 14141 . TCA CCC 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X1M1X;DP=3;DPRA=0;EPP=5.18177;EPPR=7.35324;HWE=-0;LEN=3;MEANALT=1;MQM=0;MQMR=9;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=1;PAIREDR=0;RO=2;RPP=5.18177;RPPR=3.0103;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=complex;XAI=0.0365854;XAM=0.097561;XAS=0.0609756;XRI=0;XRM=0.025;XRS=0.025 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23 +Chr1 14159 . G A 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=9;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=1;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0.0487805;XAM=0.097561;XAS=0.0487805;XRI=0;XRM=0.025;XRS=0.025 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23 +Chr1 14165 . T G 7.01833 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=2;MQM=18;MQMR=0;NS=1;NUMALT=1;ODDS=0;PAIRED=0;PAIREDR=1;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0.0487805;XRM=0.109756;XRS=0.0609756;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:0.628068:3:1:17:1:17:-3.23,-2.00103,-3.23 +Chr1 14167 . A T 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=9;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=1;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0.0487805;XAM=0.097561;XAS=0.0487805;XRI=0;XRM=0.025;XRS=0.025 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23 +Chr1 14182 . T G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=1;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0.0487805;XAM=0.097561;XAS=0.0487805;XRI=0;XRM=0.04;XRS=0.04;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 14201 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 14210 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 14230 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=1;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0222222;XAM=0.133333;XAS=0.111111;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 14240 . C T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=1;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0222222;XAM=0.133333;XAS=0.111111;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 14247 . G A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=1;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0222222;XAM=0.133333;XAS=0.111111;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 14256 . A G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=1;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0222222;XAM=0.133333;XAS=0.111111;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 14262 . TT CC 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=2X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=2;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=1;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=mnp;XAI=0.0222222;XAM=0.122222;XAS=0.1;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 14292 . TCTG CCTA 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X2M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=4;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=1;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0.0111111;XAM=0.133333;XAS=0.122222;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 14306 . AC TT 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=2X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=2;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=1;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=mnp;XAI=0.0222222;XAM=0.122222;XAS=0.1;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 14312 . CG TA 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=2X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=2;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=1;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=mnp;XAI=0.0222222;XAM=0.122222;XAS=0.1;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 14320 . TCTTT TCCCTA 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1M1I1M1X1M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=5;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=1;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0.0111111;XAM=0.133333;XAS=0.122222;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 14327 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=1;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0222222;XAM=0.133333;XAS=0.111111;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 14595 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=25;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 14624 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=25;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 14629 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=25;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 14724 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 15170 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 15183 . T A 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0.0103093;XRM=0.0206186;XRS=0.0103093;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 15199 . CAA AAT 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X1M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=3;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0.0103093;XAS=0.0103093;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 15209 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0103093;XAM=0.0103093;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 15599 . TGG GGC 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X1M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=3;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0.0103093;XAS=0.0103093;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 15624 . A T 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=40;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0.0103093;XAM=0.0103093;XAS=0;XRI=0;XRM=0.04;XRS=0.04;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 15625 . A C 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0.0103093;XRM=0.0206186;XRS=0.0103093;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 15670 . C G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0.0103093;XRM=0.0206186;XRS=0.0103093;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 15685 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 15696 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 15981 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0105263;XAM=0.0315789;XAS=0.0210526;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 16021 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0105263;XAM=0.0315789;XAS=0.0210526;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 16050 . CTGGG ATGGC 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X3M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=5;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0.0315789;XAS=0.0315789;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 16059 . A T 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0.0105263;XAM=0.0315789;XAS=0.0210526;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 16085 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 16287 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 16502 . GCA CCT 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X1M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=3;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0.0108696;XAM=0.0217391;XAS=0.0108696;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 16512 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0217391;XAM=0.0217391;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 16519 . TGTGT GGTGG 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X3M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=5;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0.0108696;XAM=0.0217391;XAS=0.0108696;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 17672 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=25;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 17738 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=25;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 17849 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 17873 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 17878 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 18083 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 18090 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 18099 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 18205 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 18275 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 18285 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 18320 . G C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 18370 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 18416 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 20586 . G T 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=27;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 20604 . T A 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=27;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 20625 . G T 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=7.35324;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=13.5;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=7.35324;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0.01;XRS=0.01 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23 +Chr1 20692 . A C 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 20702 . T A 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 20720 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 20891 . G C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=25;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 20922 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=25;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 20967 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=25;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 20998 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 21007 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 21042 . C A 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=21;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0.04;XRS=0.04;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 21055 . G A 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=21;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 21080 . C A 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=21;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 21165 . T A 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=25;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0.0104167;XAM=0.0104167;XAS=0;XRI=0;XRM=0.02;XRS=0.02;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 21189 . T G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=25;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0.0104167;XRM=0.0208333;XRS=0.0104167;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 21202 . ACCT CCCA,TCCT 20.1741 . AB=0.5,0.5;ABP=3.0103,3.0103;AC=1,1;AF=0.5,0.5;AN=2;AO=1,1;CIGAR=1X2M1X,1X3M;DP=2;DPRA=0,0;EPP=5.18177,5.18177;EPPR=0;HWE=-0;LEN=4,1;MEANALT=2,2;MQM=25,42;MQMR=0;NS=1;NUMALT=2;ODDS=0.00237165;PAIRED=0,0;PAIREDR=0;RO=0;RPP=5.18177,5.18177;RPPR=0;RUN=1,1;SAP=5.18177,5.18177;SRP=0;TYPE=complex,snp;XAI=0,0;XAM=0.0104167,0.02;XAS=0.0104167,0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/2:1.71537:2:0:0:1,1:17,17:-3.23,-2.00103,-1.7,-2.00103,-0.30103,-1.7 +Chr1 21322 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 21342 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 21359 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 21584 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 21615 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 21821 . G C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=21;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 21936 . TGT AGA 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X1M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=3;MEANALT=1;MQM=21;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0.0103093;XAS=0.0103093;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 21955 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=21;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0103093;XAM=0.0103093;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 22337 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 22345 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 22415 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0104167;XAM=0.0104167;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 22429 . ATTG CTTT 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X2M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=4;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0.0104167;XAS=0.0104167;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 22520 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 22539 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 22742 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 22801 . G C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 22888 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 22919 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 23346 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=11;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 23360 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=11;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 23390 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=11;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 23432 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=11;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 23687 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 23716 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 23745 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 23812 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 23829 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 23959 . TC AG 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=2X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=2;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=mnp;XAI=0.0104167;XAM=0.0104167;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 23989 . ATCT CTCA 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X2M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=4;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0.0208333;XAS=0.0208333;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 24095 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=26;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 24350 . G C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 24377 . G C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 24395 . A T 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0.0104167;XRM=0.03125;XRS=0.0208333;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 24413 . T G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0.0104167;XRM=0.03125;XRS=0.0208333;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 24416 . GAGT TAGA 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X2M1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=4;MEANALT=1;MQM=0;MQMR=40;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=complex;XAI=0;XAM=0.0208333;XAS=0.0208333;XRI=0;XRM=0.04;XRS=0.04;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 24467 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0104167;XAM=0.0208333;XAS=0.0104167;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 24477 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0104167;XAM=0.0208333;XAS=0.0104167;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 24846 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 24889 . A C 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 24923 . T A 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 24964 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 25174 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 25301 . A T 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 25320 . G C 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 25345 . T G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 25355 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 25550 . A T 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=25;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 25580 . A T 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=25;MQMR=20;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=3.0103;RUN=1;SAP=5.18177;SRP=7.35324;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0.00520833;XRM=0.015625;XRS=0.0104167 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23 +Chr1 25584 . C G 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=12.5;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0.0104167;XAM=0.0208333;XAS=0.0104167;XRI=0;XRM=0.01;XRS=0.01 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23 +Chr1 25626 . GCAC TCAG 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X2M1X;DP=3;DPRA=0;EPP=5.18177;EPPR=7.35324;HWE=-0;LEN=4;MEANALT=1;MQM=40;MQMR=33.5;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=7.35324;TYPE=complex;XAI=0;XAM=0.0208333;XAS=0.0208333;XRI=0.00526316;XRM=0.0205263;XRS=0.0152632 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23 +Chr1 25644 . A C 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=34.5;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0.0104167;XAM=0.0208333;XAS=0.0104167;XRI=0.00526316;XRM=0.0155263;XRS=0.0102632 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23 +Chr1 25687 . A T 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=27;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0.0105263;XAM=0.0105263;XAS=0;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 25696 . ACTCA GCTCT,GCTCA 20.1741 . AB=0.5,0.5;ABP=3.0103,3.0103;AC=1,1;AF=0.5,0.5;AN=2;AO=1,1;CIGAR=1X3M1X,1X4M;DP=2;DPRA=0,0;EPP=5.18177,5.18177;EPPR=0;HWE=-0;LEN=5,1;MEANALT=2,2;MQM=42,27;MQMR=0;NS=1;NUMALT=2;ODDS=0.00237165;PAIRED=0,0;PAIREDR=0;RO=0;RPP=5.18177,5.18177;RPPR=0;RUN=1,1;SAP=5.18177,5.18177;SRP=0;TYPE=complex,snp;XAI=0,0;XAM=0.0105263,0.01;XAS=0.0105263,0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/2:1.71537:2:0:0:1,1:17,17:-3.23,-2.00103,-1.7,-2.00103,-0.30103,-1.7 +Chr1 25944 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 25972 . G C 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 25981 . G T 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=21;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=3.0103;RUN=1;SAP=5.18177;SRP=7.35324;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0.025;XRS=0.025 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23 +Chr1 25983 . AA TT 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=2X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=2;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=mnp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.015;XRS=0.015 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23 +Chr1 26001 . G C 1.76687 . AB=0.25;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=4;DPRA=0;EPP=5.18177;EPPR=3.73412;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=0.690776;PAIRED=0;PAIREDR=0;RO=3;RPP=5.18177;RPPR=9.52472;RUN=1;SAP=5.18177;SRP=3.73412;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0.01;XRS=0.01 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76309:4:3:51:1:17:-1.7,-0.60206,-4.76 +Chr1 26364 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=25;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 26420 . G C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=25;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 27175 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 27431 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 27472 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 27556 . A AT 46.0861 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1M1I;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=ins;XAI=0;XAM=0.0102041;XAS=0.0102041;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:17.0704:1:0:0:1:46:-4.6,-0.30103,0 +Chr1 27610 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0102041;XAM=0.0102041;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 27909 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 28614 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 28993 . TGGG GGGC 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X2M1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=4;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=complex;XAI=0;XAM=0.0208333;XAS=0.0208333;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 29022 . T A 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0.00520833;XRM=0.015625;XRS=0.0104167 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23 +Chr1 29026 . T G 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=7.35324;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=7.35324;TYPE=snp;XAI=0.0104167;XAM=0.0208333;XAS=0.0104167;XRI=0;XRM=0.01;XRS=0.01 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23 +Chr1 29032 . T G 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=7.35324;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=7.35324;TYPE=snp;XAI=0.0104167;XAM=0.0208333;XAS=0.0104167;XRI=0;XRM=0.01;XRS=0.01 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23 +Chr1 29080 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 29218 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 29342 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 29463 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 29516 . T G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.03;XRS=0.03;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 29528 . T G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0.02;XRS=0.02;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 29575 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 29580 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 30681 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0105263;XAM=0.0210526;XAS=0.0105263;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 30735 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0105263;XAM=0.0210526;XAS=0.0105263;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 30766 . CTATT GTATA 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X3M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=5;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0.0210526;XAS=0.0210526;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 31019 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 31054 . G C 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 31101 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 31400 . GT CG 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=2X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=2;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=mnp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 31422 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 32027 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 32060 . C T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 32166 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 32226 . AA CC 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=2X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=2;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=mnp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 32480 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 32491 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 32651 . A C 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 32934 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 33054 . G C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 33109 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 33143 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 33245 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 33274 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 33377 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 33392 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 33417 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 33713 . C A 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 33746 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 35247 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 35679 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 36145 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 36591 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 37260 . AT CA 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=2X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=2;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=mnp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 37270 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 37283 . G T 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0.04;XRS=0.04;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 37284 . G T 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.03;XRS=0.03;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 37295 . A C 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0.04;XRS=0.04;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 37321 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 37610 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 37673 . G C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 38268 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 38656 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 39013 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 39023 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 39460 . T G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0.02;XRS=0.02;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 39480 . GA TC 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=2X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=2;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=mnp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0.03;XRS=0.03;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 39501 . T G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0.02;XRS=0.02;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 39508 . T G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0.02;XRS=0.02;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 41835 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 41885 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 42284 . AGTTT TGTTG 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X3M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=5;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 42628 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0222222;XAM=0.0222222;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 42637 . ATTCC CTTCG 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X3M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=5;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0.0111111;XAM=0.0222222;XAS=0.0111111;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 42652 . TTTGT ATTGA 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X3M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=5;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0.0111111;XAM=0.0222222;XAS=0.0111111;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 43145 . GG CC 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=2X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=2;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=mnp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 43164 . G C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.04;XAS=0.04;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 43173 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.04;XAS=0.04;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 43219 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.04;XAS=0.04;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 43437 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 44980 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 45144 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 45166 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 45311 . G C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 45333 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 45385 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 45419 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 45427 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 45663 . C G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 45685 . AG CT 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=2X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=2;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=mnp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 46052 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 46117 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 46251 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 46261 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 47385 . G C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 47414 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 48446 . T A 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 48526 . C G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 48789 . T A 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=6;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0.02;XRS=0.02;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 48796 . T G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=6;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.03;XRS=0.03;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 48811 . T G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=6;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.03;XRS=0.03;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 48831 . A C 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=6;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0.02;XRS=0.02;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 48838 . A C 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=6;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0.02;XRS=0.02;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 48852 . A T 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=3;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0.025;XRS=0.025 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23 +Chr1 48907 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 48936 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 49044 . G C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 49059 . A C 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=18;MQMR=20;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=3.0103;RUN=1;SAP=5.18177;SRP=7.35324;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0.00520833;XRM=0.0310417;XRS=0.0258333 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23 +Chr1 49086 . T G 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=9;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0.0104167;XAM=0.0416667;XAS=0.03125;XRI=0;XRM=0.015;XRS=0.015 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23 +Chr1 49088 . C G 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=18;MQMR=20;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=3.0103;RUN=1;SAP=5.18177;SRP=7.35324;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0.00520833;XRM=0.0310417;XRS=0.0258333 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23 +Chr1 49091 . T G 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=9;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0.0104167;XAM=0.0416667;XAS=0.03125;XRI=0;XRM=0.015;XRS=0.015 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23 +Chr1 49099 . T G 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=9;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0.0104167;XAM=0.0416667;XAS=0.03125;XRI=0;XRM=0.015;XRS=0.015 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23 +Chr1 49124 . AAAC TAAA 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X2M1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=4;MEANALT=1;MQM=40;MQMR=9;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=complex;XAI=0;XAM=0.0416667;XAS=0.0416667;XRI=0;XRM=0.015;XRS=0.015 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23 +Chr1 49134 . C A 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=9;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0.0104167;XAM=0.0416667;XAS=0.03125;XRI=0;XRM=0.015;XRS=0.015 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23 +Chr1 49493 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0105263;XAM=0.0315789;XAS=0.0210526;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 49543 . TGCAA GGCAT 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X3M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=5;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0.0315789;XAS=0.0315789;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 49553 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0105263;XAM=0.0315789;XAS=0.0210526;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 49583 . G C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0105263;XAM=0.0315789;XAS=0.0210526;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 50222 . ACAAAGA CCCACTC 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X1M1X1M3X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=7;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 50557 . T G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0.02;XRS=0.02;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 50574 . G C 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 50603 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 50790 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 50828 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 50843 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 50958 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 51330 . T G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=35;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 51606 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 51681 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 51984 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 51996 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 52061 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 53145 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 53423 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 53442 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 54071 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 54472 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 54525 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 54562 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 55358 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 55372 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 55415 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 55460 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 55491 . AA CC 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=2X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=2;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=mnp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 55917 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 56372 . G T 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 56383 . G T 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=41;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=3.0103;RUN=1;SAP=5.18177;SRP=7.35324;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.02;XRS=0.02 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23 +Chr1 56399 . A C 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 56430 . A C 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 56448 . C G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 56477 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 56586 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0102041;XAM=0.0204082;XAS=0.0102041;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 56642 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0102041;XAM=0.0204082;XAS=0.0102041;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 56672 . T TA 46.0861 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1M1I;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=ins;XAI=0;XAM=0.0204082;XAS=0.0204082;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:17.0704:1:0:0:1:46:-4.6,-0.30103,0 +Chr1 56708 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 56728 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 56743 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 56750 . G C 1.76687 . AB=0.25;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=4;DPRA=0;EPP=5.18177;EPPR=3.73412;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=28;NS=1;NUMALT=1;ODDS=0.690776;PAIRED=0;PAIREDR=0;RO=3;RPP=5.18177;RPPR=3.73412;RUN=1;SAP=5.18177;SRP=3.73412;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.02;XRS=0.02 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76309:4:3:51:1:17:-1.7,-0.60206,-4.76 +Chr1 56756 . A T 1.76687 . AB=0.25;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=4;DPRA=0;EPP=5.18177;EPPR=3.73412;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=28;NS=1;NUMALT=1;ODDS=0.690776;PAIRED=0;PAIREDR=0;RO=3;RPP=5.18177;RPPR=3.73412;RUN=1;SAP=5.18177;SRP=3.73412;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.02;XRS=0.02 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76309:4:3:51:1:17:-1.7,-0.60206,-4.76 +Chr1 56769 . A T 1.76687 . AB=0.25;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=4;DPRA=0;EPP=5.18177;EPPR=3.73412;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=28;NS=1;NUMALT=1;ODDS=0.690776;PAIRED=0;PAIREDR=0;RO=3;RPP=5.18177;RPPR=9.52472;RUN=1;SAP=5.18177;SRP=3.73412;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.0266667;XRS=0.0266667 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76309:4:3:51:1:17:-1.7,-0.60206,-4.76 +Chr1 56792 . A T 1.76687 . AB=0.25;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=4;DPRA=0;EPP=5.18177;EPPR=3.73412;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=28;NS=1;NUMALT=1;ODDS=0.690776;PAIRED=0;PAIREDR=0;RO=3;RPP=5.18177;RPPR=9.52472;RUN=1;SAP=5.18177;SRP=3.73412;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.02;XRS=0.02 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76309:4:3:51:1:17:-1.7,-0.60206,-4.76 +Chr1 56800 . A T 1.76687 . AB=0.25;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=4;DPRA=0;EPP=5.18177;EPPR=3.73412;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=28;NS=1;NUMALT=1;ODDS=0.690776;PAIRED=0;PAIREDR=0;RO=3;RPP=5.18177;RPPR=9.52472;RUN=1;SAP=5.18177;SRP=3.73412;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.02;XRS=0.02 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76309:4:3:51:1:17:-1.7,-0.60206,-4.76 +Chr1 56803 . C G 1.76687 . AB=0.25;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=4;DPRA=0;EPP=5.18177;EPPR=9.52472;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=28;NS=1;NUMALT=1;ODDS=0.690776;PAIRED=0;PAIREDR=0;RO=3;RPP=5.18177;RPPR=9.52472;RUN=1;SAP=5.18177;SRP=9.52472;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.02;XRS=0.02 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76309:4:3:51:1:17:-1.7,-0.60206,-4.76 +Chr1 56822 . A T 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=7.35324;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=21;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=7.35324;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.02;XRS=0.02 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23 +Chr1 57075 . T G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.03;XRS=0.03;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 57129 . A T 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0.02;XRS=0.02;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 57130 . A T 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.03;XRS=0.03;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 57164 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 57166 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 57533 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0105263;XAM=0.0210526;XAS=0.0105263;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 57543 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0105263;XAM=0.0210526;XAS=0.0105263;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 57561 . TTCGA ATCGC 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X3M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=5;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0.0210526;XAS=0.0210526;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 57885 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 57929 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 58372 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 58383 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 58391 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 58399 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 58807 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 58825 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 58844 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.02;XAS=0.02;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 58862 . A T 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0.03;XRS=0.03;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 59508 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0102041;XAM=0.0306122;XAS=0.0204082;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 59524 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0102041;XAM=0.0306122;XAS=0.0204082;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 59546 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0102041;XAM=0.0306122;XAS=0.0204082;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 59554 . C CG 46.0861 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1M1I;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=ins;XAI=0;XAM=0.0306122;XAS=0.0306122;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:17.0704:1:0:0:1:46:-4.6,-0.30103,0 +Chr1 61378 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 61387 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 61599 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 61652 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 61882 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0103093;XAM=0.0309278;XAS=0.0206186;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 61904 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0103093;XAM=0.0309278;XAS=0.0206186;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 61913 . AGG TGC 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X1M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=3;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0.0309278;XAS=0.0309278;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 61957 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0.0103093;XAM=0.0309278;XAS=0.0206186;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 62010 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 62056 . T A 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 62168 . CCGCC GCGCG 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X3M1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=5;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=complex;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 62290 . T A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 62446 . C G 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=42;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0.00520833;XRM=0.0152083;XRS=0.01 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23 +Chr1 62447 . CTAG ATAC 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X2M1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=4;MEANALT=1;MQM=42;MQMR=21;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=3.0103;RUN=1;SAP=5.18177;SRP=7.35324;TYPE=complex;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0.02;XRS=0.02 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23 +Chr1 62462 . C G 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=42;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0.00520833;XRM=0.0152083;XRS=0.01 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23 +Chr1 62478 . C G 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=21;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0.00520833;XRM=0.0152083;XRS=0.01 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23 +Chr1 62514 . G T 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.02;XRS=0.02;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 62598 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 62634 . T G 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=42;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.04;XRS=0.04;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 62658 . T G 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=21;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.01;XRS=0.01 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23 +Chr1 62665 . G C 2.50735 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPRA=0;EPP=5.18177;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=21;NS=1;NUMALT=1;ODDS=0.28531;PAIRED=0;PAIREDR=0;RO=2;RPP=5.18177;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=3.0103;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0.01;XRS=0.01 GT:GQ:DP:RO:QR:AO:QA:GL 0/1:2.38104:3:2:34:1:17:-1.7,-0.425969,-3.23 +Chr1 62686 . A T 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 62697 . C A 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.03;XAS=0.03;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7 +Chr1 62758 . G T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 62769 . A C 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=0;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 62841 . T G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 62852 . C G 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 62929 . C A 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=18;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 63049 . A T 17.1701 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPRA=0;EPP=5.18177;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=0;NS=1;NUMALT=1;ODDS=3.91202;PAIRED=0;PAIREDR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAP=5.18177;SRP=0;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/1:14.1547:1:0:0:1:17:-1.7,-0.30103,0 +Chr1 63120 . C A 4.77465 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPRA=0;EPP=5.18177;EPPR=5.18177;HWE=-0;LEN=1;MEANALT=1;MQM=42;MQMR=18;NS=1;NUMALT=1;ODDS=0.00237165;PAIRED=0;PAIREDR=0;RO=1;RPP=5.18177;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.01;XAS=0.01;XRI=0;XRM=0.01;XRS=0.01;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 0/1:1.76435:2:1:17:1:17:-1.7,-0.30103,-1.7
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/freebayes_vcf_to_gff_output.gff Thu May 22 20:30:19 2014 -0400 @@ -0,0 +1,449 @@ +#gff-version 3 +Chr1 SAMTOOLS SNP 106 106 17.1701 . . ID=Chr1:SNP:106;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 200 200 17.1701 . . ID=Chr1:SNP:200;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 217 217 4.77465 . . ID=Chr1:SNP:217;Variant_seq=T;Reference_seq=G;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 249 249 4.77465 . . ID=Chr1:SNP:249;Variant_seq=A;Reference_seq=T;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 586 586 17.1701 . . ID=Chr1:SNP:586;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 669 669 4.77465 . . ID=Chr1:SNP:669;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 682 682 4.77465 . . ID=Chr1:SNP:682;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 1007 1007 17.1701 . . ID=Chr1:SNP:1007;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 1012 1012 17.1701 . . ID=Chr1:SNP:1012;Variant_seq=AGA;Reference_seq=TGT;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 1056 1056 17.1701 . . ID=Chr1:SNP:1056;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 1067 1067 17.1701 . . ID=Chr1:SNP:1067;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 1257 1257 17.1701 . . ID=Chr1:SNP:1257;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 1305 1305 17.1701 . . ID=Chr1:SNP:1305;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 1319 1319 17.1701 . . ID=Chr1:SNP:1319;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 1330 1330 17.1701 . . ID=Chr1:SNP:1330;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 1441 1441 17.1701 . . ID=Chr1:SNP:1441;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 1451 1451 17.1701 . . ID=Chr1:SNP:1451;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 1460 1460 17.1701 . . ID=Chr1:SNP:1460;Variant_seq=ATCTC;Reference_seq=CTCTG;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 1480 1480 17.1701 . . ID=Chr1:SNP:1480;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 1525 1525 17.1701 . . ID=Chr1:SNP:1525;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 1670 1670 4.77465 . . ID=Chr1:SNP:1670;Variant_seq=T;Reference_seq=G;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 1673 1673 4.77465 . . ID=Chr1:SNP:1673;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 1700 1700 4.77465 . . ID=Chr1:SNP:1700;Variant_seq=TG;Reference_seq=GC;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 1711 1711 4.77465 . . ID=Chr1:SNP:1711;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 2117 2117 17.1701 . . ID=Chr1:SNP:2117;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 2154 2154 17.1701 . . ID=Chr1:SNP:2154;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 2485 2485 17.1701 . . ID=Chr1:SNP:2485;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 2490 2490 17.1701 . . ID=Chr1:SNP:2490;Variant_seq=CAC;Reference_seq=AAA;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 2906 2906 17.1701 . . ID=Chr1:SNP:2906;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 2925 2925 17.1701 . . ID=Chr1:SNP:2925;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 3371 3371 17.1701 . . ID=Chr1:SNP:3371;Variant_seq=GCCTA;Reference_seq=CCCTT;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 3389 3389 17.1701 . . ID=Chr1:SNP:3389;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 3431 3431 17.1701 . . ID=Chr1:SNP:3431;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 3464 3464 17.1701 . . ID=Chr1:SNP:3464;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 3746 3746 46.0861 . . ID=Chr1:SNP:3746;Variant_seq=CT;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 3766 3766 4.77465 . . ID=Chr1:SNP:3766;Variant_seq=A;Reference_seq=C;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 3790 3790 4.77465 . . ID=Chr1:SNP:3790;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 3855 3855 17.1701 . . ID=Chr1:SNP:3855;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 5718 5718 17.1701 . . ID=Chr1:SNP:5718;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 5754 5754 17.1701 . . ID=Chr1:SNP:5754;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 5782 5782 17.1701 . . ID=Chr1:SNP:5782;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 5792 5792 17.1701 . . ID=Chr1:SNP:5792;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 6194 6194 17.1701 . . ID=Chr1:SNP:6194;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 6212 6212 17.1701 . . ID=Chr1:SNP:6212;Variant_seq=A;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 6265 6265 17.1701 . . ID=Chr1:SNP:6265;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 6482 6482 17.1701 . . ID=Chr1:SNP:6482;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 6515 6515 17.1701 . . ID=Chr1:SNP:6515;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 6520 6520 17.1701 . . ID=Chr1:SNP:6520;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 6534 6534 17.1701 . . ID=Chr1:SNP:6534;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 6602 6602 17.1701 . . ID=Chr1:SNP:6602;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 6853 6853 17.1701 . . ID=Chr1:SNP:6853;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 7015 7015 17.1701 . . ID=Chr1:SNP:7015;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 7406 7406 17.1701 . . ID=Chr1:SNP:7406;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 7422 7422 17.1701 . . ID=Chr1:SNP:7422;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 7452 7452 17.1701 . . ID=Chr1:SNP:7452;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 7460 7460 17.1701 . . ID=Chr1:SNP:7460;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 7476 7476 17.1701 . . ID=Chr1:SNP:7476;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 7843 7843 17.1701 . . ID=Chr1:SNP:7843;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 7906 7906 17.1701 . . ID=Chr1:SNP:7906;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 8214 8214 17.1701 . . ID=Chr1:SNP:8214;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 8262 8262 17.1701 . . ID=Chr1:SNP:8262;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 8279 8279 4.77465 . . ID=Chr1:SNP:8279;Variant_seq=T;Reference_seq=G;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 8285 8285 4.77465 . . ID=Chr1:SNP:8285;Variant_seq=G;Reference_seq=C;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 8288 8288 4.77465 . . ID=Chr1:SNP:8288;Variant_seq=C;Reference_seq=G;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 8298 8298 4.77465 . . ID=Chr1:SNP:8298;Variant_seq=C;Reference_seq=G;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 8305 8305 4.77465 . . ID=Chr1:SNP:8305;Variant_seq=C;Reference_seq=G;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 8329 8329 17.1701 . . ID=Chr1:SNP:8329;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 8509 8509 17.1701 . . ID=Chr1:SNP:8509;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 8547 8547 17.1701 . . ID=Chr1:SNP:8547;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 8633 8633 17.1701 . . ID=Chr1:SNP:8633;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 8657 8657 17.1701 . . ID=Chr1:SNP:8657;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 8894 8894 17.1701 . . ID=Chr1:SNP:8894;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 8958 8958 17.1701 . . ID=Chr1:SNP:8958;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 8968 8968 17.1701 . . ID=Chr1:SNP:8968;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 9070 9070 17.1701 . . ID=Chr1:SNP:9070;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 9100 9100 17.1701 . . ID=Chr1:SNP:9100;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 9488 9488 17.1701 . . ID=Chr1:SNP:9488;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 9514 9514 4.77465 . . ID=Chr1:SNP:9514;Variant_seq=CTTG;Reference_seq=GTTT;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 9532 9532 4.77465 . . ID=Chr1:SNP:9532;Variant_seq=T;Reference_seq=A;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 10064 10064 17.1701 . . ID=Chr1:SNP:10064;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 10072 10072 17.1701 . . ID=Chr1:SNP:10072;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 10082 10082 17.1701 . . ID=Chr1:SNP:10082;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 10099 10099 17.1701 . . ID=Chr1:SNP:10099;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 10499 10499 17.1701 . . ID=Chr1:SNP:10499;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 11126 11126 4.77465 . . ID=Chr1:SNP:11126;Variant_seq=G;Reference_seq=C;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 11134 11134 4.77465 . . ID=Chr1:SNP:11134;Variant_seq=C;Reference_seq=A;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 11141 11141 4.77465 . . ID=Chr1:SNP:11141;Variant_seq=G;Reference_seq=C;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 11159 11159 4.77465 . . ID=Chr1:SNP:11159;Variant_seq=G;Reference_seq=C;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 11169 11169 4.77465 . . ID=Chr1:SNP:11169;Variant_seq=C;Reference_seq=A;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 11208 11208 17.1701 . . ID=Chr1:SNP:11208;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 11418 11418 17.1701 . . ID=Chr1:SNP:11418;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 11547 11547 4.77465 . . ID=Chr1:SNP:11547;Variant_seq=T;Reference_seq=A;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 11567 11567 4.77465 . . ID=Chr1:SNP:11567;Variant_seq=A;Reference_seq=C;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 11582 11582 17.1701 . . ID=Chr1:SNP:11582;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 13312 13312 17.1701 . . ID=Chr1:SNP:13312;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 13336 13336 17.1701 . . ID=Chr1:SNP:13336;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 13352 13352 17.1701 . . ID=Chr1:SNP:13352;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 13652 13652 17.1701 . . ID=Chr1:SNP:13652;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 13666 13666 17.1701 . . ID=Chr1:SNP:13666;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 13728 13728 4.77465 . . ID=Chr1:SNP:13728;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 14087 14087 4.77465 . . ID=Chr1:SNP:14087;Variant_seq=GTGAGC;Reference_seq=ATGAAA;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 14103 14103 4.77465 . . ID=Chr1:SNP:14103;Variant_seq=GGC;Reference_seq=AGT;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 14119 14119 4.77465 . . ID=Chr1:SNP:14119;Variant_seq=T;Reference_seq=A;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 14126 14126 4.77465 . . ID=Chr1:SNP:14126;Variant_seq=G;Reference_seq=A;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 14131 14131 2.50735 . . ID=Chr1:SNP:14131;Variant_seq=TGGGTT;Reference_seq=GGAGTG;Total_reads=3;Zygosity=3:HET +Chr1 SAMTOOLS SNP 14141 14141 2.50735 . . ID=Chr1:SNP:14141;Variant_seq=CCC;Reference_seq=TCA;Total_reads=3;Zygosity=3:HET +Chr1 SAMTOOLS SNP 14159 14159 2.50735 . . ID=Chr1:SNP:14159;Variant_seq=A;Reference_seq=G;Total_reads=3;Zygosity=3:HET +Chr1 SAMTOOLS SNP 14165 14165 7.01833 . . ID=Chr1:SNP:14165;Variant_seq=G;Reference_seq=T;Total_reads=3;Zygosity=3:HOM_mut +Chr1 SAMTOOLS SNP 14167 14167 2.50735 . . ID=Chr1:SNP:14167;Variant_seq=T;Reference_seq=A;Total_reads=3;Zygosity=3:HET +Chr1 SAMTOOLS SNP 14182 14182 4.77465 . . ID=Chr1:SNP:14182;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 14201 14201 17.1701 . . ID=Chr1:SNP:14201;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 14210 14210 17.1701 . . ID=Chr1:SNP:14210;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 14230 14230 17.1701 . . ID=Chr1:SNP:14230;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 14240 14240 17.1701 . . ID=Chr1:SNP:14240;Variant_seq=T;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 14247 14247 17.1701 . . ID=Chr1:SNP:14247;Variant_seq=A;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 14256 14256 17.1701 . . ID=Chr1:SNP:14256;Variant_seq=G;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 14262 14262 17.1701 . . ID=Chr1:SNP:14262;Variant_seq=CC;Reference_seq=TT;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 14292 14292 17.1701 . . ID=Chr1:SNP:14292;Variant_seq=CCTA;Reference_seq=TCTG;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 14306 14306 17.1701 . . ID=Chr1:SNP:14306;Variant_seq=TT;Reference_seq=AC;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 14312 14312 17.1701 . . ID=Chr1:SNP:14312;Variant_seq=TA;Reference_seq=CG;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 14320 14320 17.1701 . . ID=Chr1:SNP:14320;Variant_seq=TCCCTA;Reference_seq=TCTTT;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 14327 14327 17.1701 . . ID=Chr1:SNP:14327;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 14595 14595 17.1701 . . ID=Chr1:SNP:14595;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 14624 14624 17.1701 . . ID=Chr1:SNP:14624;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 14629 14629 17.1701 . . ID=Chr1:SNP:14629;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 14724 14724 17.1701 . . ID=Chr1:SNP:14724;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 15170 15170 17.1701 . . ID=Chr1:SNP:15170;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 15183 15183 4.77465 . . ID=Chr1:SNP:15183;Variant_seq=A;Reference_seq=T;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 15199 15199 17.1701 . . ID=Chr1:SNP:15199;Variant_seq=AAT;Reference_seq=CAA;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 15209 15209 17.1701 . . ID=Chr1:SNP:15209;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 15599 15599 17.1701 . . ID=Chr1:SNP:15599;Variant_seq=GGC;Reference_seq=TGG;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 15624 15624 4.77465 . . ID=Chr1:SNP:15624;Variant_seq=T;Reference_seq=A;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 15625 15625 4.77465 . . ID=Chr1:SNP:15625;Variant_seq=C;Reference_seq=A;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 15670 15670 4.77465 . . ID=Chr1:SNP:15670;Variant_seq=G;Reference_seq=C;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 15685 15685 17.1701 . . ID=Chr1:SNP:15685;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 15696 15696 17.1701 . . ID=Chr1:SNP:15696;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 15981 15981 17.1701 . . ID=Chr1:SNP:15981;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 16021 16021 17.1701 . . ID=Chr1:SNP:16021;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 16050 16050 17.1701 . . ID=Chr1:SNP:16050;Variant_seq=ATGGC;Reference_seq=CTGGG;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 16059 16059 4.77465 . . ID=Chr1:SNP:16059;Variant_seq=T;Reference_seq=A;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 16085 16085 17.1701 . . ID=Chr1:SNP:16085;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 16287 16287 17.1701 . . ID=Chr1:SNP:16287;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 16502 16502 17.1701 . . ID=Chr1:SNP:16502;Variant_seq=CCT;Reference_seq=GCA;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 16512 16512 17.1701 . . ID=Chr1:SNP:16512;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 16519 16519 17.1701 . . ID=Chr1:SNP:16519;Variant_seq=GGTGG;Reference_seq=TGTGT;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 17672 17672 17.1701 . . ID=Chr1:SNP:17672;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 17738 17738 17.1701 . . ID=Chr1:SNP:17738;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 17849 17849 17.1701 . . ID=Chr1:SNP:17849;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 17873 17873 17.1701 . . ID=Chr1:SNP:17873;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 17878 17878 17.1701 . . ID=Chr1:SNP:17878;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 18083 18083 17.1701 . . ID=Chr1:SNP:18083;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 18090 18090 17.1701 . . ID=Chr1:SNP:18090;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 18099 18099 17.1701 . . ID=Chr1:SNP:18099;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 18205 18205 17.1701 . . ID=Chr1:SNP:18205;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 18275 18275 17.1701 . . ID=Chr1:SNP:18275;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 18285 18285 17.1701 . . ID=Chr1:SNP:18285;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 18320 18320 17.1701 . . ID=Chr1:SNP:18320;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 18370 18370 17.1701 . . ID=Chr1:SNP:18370;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 18416 18416 17.1701 . . ID=Chr1:SNP:18416;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 20586 20586 4.77465 . . ID=Chr1:SNP:20586;Variant_seq=T;Reference_seq=G;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 20604 20604 4.77465 . . ID=Chr1:SNP:20604;Variant_seq=A;Reference_seq=T;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 20625 20625 2.50735 . . ID=Chr1:SNP:20625;Variant_seq=T;Reference_seq=G;Total_reads=3;Zygosity=3:HET +Chr1 SAMTOOLS SNP 20692 20692 4.77465 . . ID=Chr1:SNP:20692;Variant_seq=C;Reference_seq=A;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 20702 20702 4.77465 . . ID=Chr1:SNP:20702;Variant_seq=A;Reference_seq=T;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 20720 20720 17.1701 . . ID=Chr1:SNP:20720;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 20891 20891 17.1701 . . ID=Chr1:SNP:20891;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 20922 20922 17.1701 . . ID=Chr1:SNP:20922;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 20967 20967 17.1701 . . ID=Chr1:SNP:20967;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 20998 20998 17.1701 . . ID=Chr1:SNP:20998;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 21007 21007 17.1701 . . ID=Chr1:SNP:21007;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 21042 21042 4.77465 . . ID=Chr1:SNP:21042;Variant_seq=A;Reference_seq=C;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 21055 21055 4.77465 . . ID=Chr1:SNP:21055;Variant_seq=A;Reference_seq=G;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 21080 21080 4.77465 . . ID=Chr1:SNP:21080;Variant_seq=A;Reference_seq=C;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 21165 21165 4.77465 . . ID=Chr1:SNP:21165;Variant_seq=A;Reference_seq=T;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 21189 21189 4.77465 . . ID=Chr1:SNP:21189;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 21202 21202 20.1741 . . ID=Chr1:SNP:21202;Variant_seq=CCCA,TCCT;Reference_seq=ACCT;Total_reads=2;Zygosity=2:NA +Chr1 SAMTOOLS SNP 21322 21322 17.1701 . . ID=Chr1:SNP:21322;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 21342 21342 17.1701 . . ID=Chr1:SNP:21342;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 21359 21359 17.1701 . . ID=Chr1:SNP:21359;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 21584 21584 17.1701 . . ID=Chr1:SNP:21584;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 21615 21615 17.1701 . . ID=Chr1:SNP:21615;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 21821 21821 17.1701 . . ID=Chr1:SNP:21821;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 21936 21936 17.1701 . . ID=Chr1:SNP:21936;Variant_seq=AGA;Reference_seq=TGT;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 21955 21955 17.1701 . . ID=Chr1:SNP:21955;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 22337 22337 17.1701 . . ID=Chr1:SNP:22337;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 22345 22345 17.1701 . . ID=Chr1:SNP:22345;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 22415 22415 17.1701 . . ID=Chr1:SNP:22415;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 22429 22429 17.1701 . . ID=Chr1:SNP:22429;Variant_seq=CTTT;Reference_seq=ATTG;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 22520 22520 17.1701 . . ID=Chr1:SNP:22520;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 22539 22539 17.1701 . . ID=Chr1:SNP:22539;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 22742 22742 17.1701 . . ID=Chr1:SNP:22742;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 22801 22801 17.1701 . . ID=Chr1:SNP:22801;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 22888 22888 17.1701 . . ID=Chr1:SNP:22888;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 22919 22919 17.1701 . . ID=Chr1:SNP:22919;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 23346 23346 17.1701 . . ID=Chr1:SNP:23346;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 23360 23360 17.1701 . . ID=Chr1:SNP:23360;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 23390 23390 17.1701 . . ID=Chr1:SNP:23390;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 23432 23432 17.1701 . . ID=Chr1:SNP:23432;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 23687 23687 17.1701 . . ID=Chr1:SNP:23687;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 23716 23716 17.1701 . . ID=Chr1:SNP:23716;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 23745 23745 17.1701 . . ID=Chr1:SNP:23745;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 23812 23812 17.1701 . . ID=Chr1:SNP:23812;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 23829 23829 17.1701 . . ID=Chr1:SNP:23829;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 23959 23959 17.1701 . . ID=Chr1:SNP:23959;Variant_seq=AG;Reference_seq=TC;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 23989 23989 17.1701 . . ID=Chr1:SNP:23989;Variant_seq=CTCA;Reference_seq=ATCT;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 24095 24095 17.1701 . . ID=Chr1:SNP:24095;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 24350 24350 17.1701 . . ID=Chr1:SNP:24350;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 24377 24377 17.1701 . . ID=Chr1:SNP:24377;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 24395 24395 4.77465 . . ID=Chr1:SNP:24395;Variant_seq=T;Reference_seq=A;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 24413 24413 4.77465 . . ID=Chr1:SNP:24413;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 24416 24416 4.77465 . . ID=Chr1:SNP:24416;Variant_seq=TAGA;Reference_seq=GAGT;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 24467 24467 17.1701 . . ID=Chr1:SNP:24467;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 24477 24477 17.1701 . . ID=Chr1:SNP:24477;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 24846 24846 17.1701 . . ID=Chr1:SNP:24846;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 24889 24889 4.77465 . . ID=Chr1:SNP:24889;Variant_seq=C;Reference_seq=A;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 24923 24923 4.77465 . . ID=Chr1:SNP:24923;Variant_seq=A;Reference_seq=T;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 24964 24964 17.1701 . . ID=Chr1:SNP:24964;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 25174 25174 17.1701 . . ID=Chr1:SNP:25174;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 25301 25301 4.77465 . . ID=Chr1:SNP:25301;Variant_seq=T;Reference_seq=A;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 25320 25320 4.77465 . . ID=Chr1:SNP:25320;Variant_seq=C;Reference_seq=G;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 25345 25345 4.77465 . . ID=Chr1:SNP:25345;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 25355 25355 17.1701 . . ID=Chr1:SNP:25355;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 25550 25550 4.77465 . . ID=Chr1:SNP:25550;Variant_seq=T;Reference_seq=A;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 25580 25580 2.50735 . . ID=Chr1:SNP:25580;Variant_seq=T;Reference_seq=A;Total_reads=3;Zygosity=3:HET +Chr1 SAMTOOLS SNP 25584 25584 2.50735 . . ID=Chr1:SNP:25584;Variant_seq=G;Reference_seq=C;Total_reads=3;Zygosity=3:HET +Chr1 SAMTOOLS SNP 25626 25626 2.50735 . . ID=Chr1:SNP:25626;Variant_seq=TCAG;Reference_seq=GCAC;Total_reads=3;Zygosity=3:HET +Chr1 SAMTOOLS SNP 25644 25644 2.50735 . . ID=Chr1:SNP:25644;Variant_seq=C;Reference_seq=A;Total_reads=3;Zygosity=3:HET +Chr1 SAMTOOLS SNP 25687 25687 4.77465 . . ID=Chr1:SNP:25687;Variant_seq=T;Reference_seq=A;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 25696 25696 20.1741 . . ID=Chr1:SNP:25696;Variant_seq=GCTCT,GCTCA;Reference_seq=ACTCA;Total_reads=2;Zygosity=2:NA +Chr1 SAMTOOLS SNP 25944 25944 17.1701 . . ID=Chr1:SNP:25944;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 25972 25972 4.77465 . . ID=Chr1:SNP:25972;Variant_seq=C;Reference_seq=G;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 25981 25981 2.50735 . . ID=Chr1:SNP:25981;Variant_seq=T;Reference_seq=G;Total_reads=3;Zygosity=3:HET +Chr1 SAMTOOLS SNP 25983 25983 2.50735 . . ID=Chr1:SNP:25983;Variant_seq=TT;Reference_seq=AA;Total_reads=3;Zygosity=3:HET +Chr1 SAMTOOLS SNP 26001 26001 1.76687 . . ID=Chr1:SNP:26001;Variant_seq=C;Reference_seq=G;Total_reads=4;Zygosity=4:HET +Chr1 SAMTOOLS SNP 26364 26364 17.1701 . . ID=Chr1:SNP:26364;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 26420 26420 17.1701 . . ID=Chr1:SNP:26420;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 27175 27175 17.1701 . . ID=Chr1:SNP:27175;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 27431 27431 17.1701 . . ID=Chr1:SNP:27431;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 27472 27472 17.1701 . . ID=Chr1:SNP:27472;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 27556 27556 46.0861 . . ID=Chr1:SNP:27556;Variant_seq=AT;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 27610 27610 17.1701 . . ID=Chr1:SNP:27610;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 27909 27909 17.1701 . . ID=Chr1:SNP:27909;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 28614 28614 17.1701 . . ID=Chr1:SNP:28614;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 28993 28993 4.77465 . . ID=Chr1:SNP:28993;Variant_seq=GGGC;Reference_seq=TGGG;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 29022 29022 2.50735 . . ID=Chr1:SNP:29022;Variant_seq=A;Reference_seq=T;Total_reads=3;Zygosity=3:HET +Chr1 SAMTOOLS SNP 29026 29026 2.50735 . . ID=Chr1:SNP:29026;Variant_seq=G;Reference_seq=T;Total_reads=3;Zygosity=3:HET +Chr1 SAMTOOLS SNP 29032 29032 2.50735 . . ID=Chr1:SNP:29032;Variant_seq=G;Reference_seq=T;Total_reads=3;Zygosity=3:HET +Chr1 SAMTOOLS SNP 29080 29080 17.1701 . . ID=Chr1:SNP:29080;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 29218 29218 17.1701 . . ID=Chr1:SNP:29218;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 29342 29342 17.1701 . . ID=Chr1:SNP:29342;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 29463 29463 17.1701 . . ID=Chr1:SNP:29463;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 29516 29516 4.77465 . . ID=Chr1:SNP:29516;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 29528 29528 4.77465 . . ID=Chr1:SNP:29528;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 29575 29575 17.1701 . . ID=Chr1:SNP:29575;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 29580 29580 17.1701 . . ID=Chr1:SNP:29580;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 30681 30681 17.1701 . . ID=Chr1:SNP:30681;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 30735 30735 17.1701 . . ID=Chr1:SNP:30735;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 30766 30766 17.1701 . . ID=Chr1:SNP:30766;Variant_seq=GTATA;Reference_seq=CTATT;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 31019 31019 17.1701 . . ID=Chr1:SNP:31019;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 31054 31054 4.77465 . . ID=Chr1:SNP:31054;Variant_seq=C;Reference_seq=G;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 31101 31101 17.1701 . . ID=Chr1:SNP:31101;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 31400 31400 17.1701 . . ID=Chr1:SNP:31400;Variant_seq=CG;Reference_seq=GT;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 31422 31422 17.1701 . . ID=Chr1:SNP:31422;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 32027 32027 17.1701 . . ID=Chr1:SNP:32027;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 32060 32060 17.1701 . . ID=Chr1:SNP:32060;Variant_seq=T;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 32166 32166 17.1701 . . ID=Chr1:SNP:32166;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 32226 32226 17.1701 . . ID=Chr1:SNP:32226;Variant_seq=CC;Reference_seq=AA;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 32480 32480 17.1701 . . ID=Chr1:SNP:32480;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 32491 32491 17.1701 . . ID=Chr1:SNP:32491;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 32651 32651 4.77465 . . ID=Chr1:SNP:32651;Variant_seq=C;Reference_seq=A;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 32934 32934 17.1701 . . ID=Chr1:SNP:32934;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 33054 33054 17.1701 . . ID=Chr1:SNP:33054;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 33109 33109 17.1701 . . ID=Chr1:SNP:33109;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 33143 33143 17.1701 . . ID=Chr1:SNP:33143;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 33245 33245 17.1701 . . ID=Chr1:SNP:33245;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 33274 33274 17.1701 . . ID=Chr1:SNP:33274;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 33377 33377 17.1701 . . ID=Chr1:SNP:33377;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 33392 33392 17.1701 . . ID=Chr1:SNP:33392;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 33417 33417 17.1701 . . ID=Chr1:SNP:33417;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 33713 33713 4.77465 . . ID=Chr1:SNP:33713;Variant_seq=A;Reference_seq=C;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 33746 33746 17.1701 . . ID=Chr1:SNP:33746;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 35247 35247 17.1701 . . ID=Chr1:SNP:35247;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 35679 35679 17.1701 . . ID=Chr1:SNP:35679;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 36145 36145 17.1701 . . ID=Chr1:SNP:36145;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 36591 36591 17.1701 . . ID=Chr1:SNP:36591;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 37260 37260 17.1701 . . ID=Chr1:SNP:37260;Variant_seq=CA;Reference_seq=AT;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 37270 37270 17.1701 . . ID=Chr1:SNP:37270;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 37283 37283 4.77465 . . ID=Chr1:SNP:37283;Variant_seq=T;Reference_seq=G;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 37284 37284 4.77465 . . ID=Chr1:SNP:37284;Variant_seq=T;Reference_seq=G;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 37295 37295 4.77465 . . ID=Chr1:SNP:37295;Variant_seq=C;Reference_seq=A;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 37321 37321 17.1701 . . ID=Chr1:SNP:37321;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 37610 37610 17.1701 . . ID=Chr1:SNP:37610;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 37673 37673 17.1701 . . ID=Chr1:SNP:37673;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 38268 38268 17.1701 . . ID=Chr1:SNP:38268;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 38656 38656 17.1701 . . ID=Chr1:SNP:38656;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 39013 39013 17.1701 . . ID=Chr1:SNP:39013;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 39023 39023 17.1701 . . ID=Chr1:SNP:39023;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 39460 39460 4.77465 . . ID=Chr1:SNP:39460;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 39480 39480 4.77465 . . ID=Chr1:SNP:39480;Variant_seq=TC;Reference_seq=GA;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 39501 39501 4.77465 . . ID=Chr1:SNP:39501;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 39508 39508 4.77465 . . ID=Chr1:SNP:39508;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 41835 41835 17.1701 . . ID=Chr1:SNP:41835;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 41885 41885 17.1701 . . ID=Chr1:SNP:41885;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 42284 42284 17.1701 . . ID=Chr1:SNP:42284;Variant_seq=TGTTG;Reference_seq=AGTTT;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 42628 42628 17.1701 . . ID=Chr1:SNP:42628;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 42637 42637 17.1701 . . ID=Chr1:SNP:42637;Variant_seq=CTTCG;Reference_seq=ATTCC;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 42652 42652 17.1701 . . ID=Chr1:SNP:42652;Variant_seq=ATTGA;Reference_seq=TTTGT;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 43145 43145 17.1701 . . ID=Chr1:SNP:43145;Variant_seq=CC;Reference_seq=GG;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 43164 43164 17.1701 . . ID=Chr1:SNP:43164;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 43173 43173 17.1701 . . ID=Chr1:SNP:43173;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 43219 43219 17.1701 . . ID=Chr1:SNP:43219;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 43437 43437 17.1701 . . ID=Chr1:SNP:43437;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 44980 44980 17.1701 . . ID=Chr1:SNP:44980;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 45144 45144 17.1701 . . ID=Chr1:SNP:45144;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 45166 45166 17.1701 . . ID=Chr1:SNP:45166;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 45311 45311 17.1701 . . ID=Chr1:SNP:45311;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 45333 45333 17.1701 . . ID=Chr1:SNP:45333;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 45385 45385 17.1701 . . ID=Chr1:SNP:45385;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 45419 45419 17.1701 . . ID=Chr1:SNP:45419;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 45427 45427 17.1701 . . ID=Chr1:SNP:45427;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 45663 45663 4.77465 . . ID=Chr1:SNP:45663;Variant_seq=G;Reference_seq=C;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 45685 45685 4.77465 . . ID=Chr1:SNP:45685;Variant_seq=CT;Reference_seq=AG;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 46052 46052 17.1701 . . ID=Chr1:SNP:46052;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 46117 46117 17.1701 . . ID=Chr1:SNP:46117;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 46251 46251 17.1701 . . ID=Chr1:SNP:46251;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 46261 46261 17.1701 . . ID=Chr1:SNP:46261;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 47385 47385 17.1701 . . ID=Chr1:SNP:47385;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 47414 47414 17.1701 . . ID=Chr1:SNP:47414;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 48446 48446 4.77465 . . ID=Chr1:SNP:48446;Variant_seq=A;Reference_seq=T;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 48526 48526 4.77465 . . ID=Chr1:SNP:48526;Variant_seq=G;Reference_seq=C;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 48789 48789 4.77465 . . ID=Chr1:SNP:48789;Variant_seq=A;Reference_seq=T;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 48796 48796 4.77465 . . ID=Chr1:SNP:48796;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 48811 48811 4.77465 . . ID=Chr1:SNP:48811;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 48831 48831 4.77465 . . ID=Chr1:SNP:48831;Variant_seq=C;Reference_seq=A;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 48838 48838 4.77465 . . ID=Chr1:SNP:48838;Variant_seq=C;Reference_seq=A;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 48852 48852 2.50735 . . ID=Chr1:SNP:48852;Variant_seq=T;Reference_seq=A;Total_reads=3;Zygosity=3:HET +Chr1 SAMTOOLS SNP 48907 48907 17.1701 . . ID=Chr1:SNP:48907;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 48936 48936 17.1701 . . ID=Chr1:SNP:48936;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 49044 49044 17.1701 . . ID=Chr1:SNP:49044;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 49059 49059 2.50735 . . ID=Chr1:SNP:49059;Variant_seq=C;Reference_seq=A;Total_reads=3;Zygosity=3:HET +Chr1 SAMTOOLS SNP 49086 49086 2.50735 . . ID=Chr1:SNP:49086;Variant_seq=G;Reference_seq=T;Total_reads=3;Zygosity=3:HET +Chr1 SAMTOOLS SNP 49088 49088 2.50735 . . ID=Chr1:SNP:49088;Variant_seq=G;Reference_seq=C;Total_reads=3;Zygosity=3:HET +Chr1 SAMTOOLS SNP 49091 49091 2.50735 . . ID=Chr1:SNP:49091;Variant_seq=G;Reference_seq=T;Total_reads=3;Zygosity=3:HET +Chr1 SAMTOOLS SNP 49099 49099 2.50735 . . ID=Chr1:SNP:49099;Variant_seq=G;Reference_seq=T;Total_reads=3;Zygosity=3:HET +Chr1 SAMTOOLS SNP 49124 49124 2.50735 . . ID=Chr1:SNP:49124;Variant_seq=TAAA;Reference_seq=AAAC;Total_reads=3;Zygosity=3:HET +Chr1 SAMTOOLS SNP 49134 49134 2.50735 . . ID=Chr1:SNP:49134;Variant_seq=A;Reference_seq=C;Total_reads=3;Zygosity=3:HET +Chr1 SAMTOOLS SNP 49493 49493 17.1701 . . ID=Chr1:SNP:49493;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 49543 49543 17.1701 . . ID=Chr1:SNP:49543;Variant_seq=GGCAT;Reference_seq=TGCAA;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 49553 49553 17.1701 . . ID=Chr1:SNP:49553;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 49583 49583 17.1701 . . ID=Chr1:SNP:49583;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 50222 50222 17.1701 . . ID=Chr1:SNP:50222;Variant_seq=CCCACTC;Reference_seq=ACAAAGA;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 50557 50557 4.77465 . . ID=Chr1:SNP:50557;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 50574 50574 4.77465 . . ID=Chr1:SNP:50574;Variant_seq=C;Reference_seq=G;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 50603 50603 17.1701 . . ID=Chr1:SNP:50603;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 50790 50790 17.1701 . . ID=Chr1:SNP:50790;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 50828 50828 17.1701 . . ID=Chr1:SNP:50828;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 50843 50843 17.1701 . . ID=Chr1:SNP:50843;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 50958 50958 17.1701 . . ID=Chr1:SNP:50958;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 51330 51330 4.77465 . . ID=Chr1:SNP:51330;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 51606 51606 17.1701 . . ID=Chr1:SNP:51606;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 51681 51681 17.1701 . . ID=Chr1:SNP:51681;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 51984 51984 17.1701 . . ID=Chr1:SNP:51984;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 51996 51996 17.1701 . . ID=Chr1:SNP:51996;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 52061 52061 17.1701 . . ID=Chr1:SNP:52061;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 53145 53145 17.1701 . . ID=Chr1:SNP:53145;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 53423 53423 17.1701 . . ID=Chr1:SNP:53423;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 53442 53442 17.1701 . . ID=Chr1:SNP:53442;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 54071 54071 17.1701 . . ID=Chr1:SNP:54071;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 54472 54472 17.1701 . . ID=Chr1:SNP:54472;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 54525 54525 17.1701 . . ID=Chr1:SNP:54525;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 54562 54562 17.1701 . . ID=Chr1:SNP:54562;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 55358 55358 17.1701 . . ID=Chr1:SNP:55358;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 55372 55372 17.1701 . . ID=Chr1:SNP:55372;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 55415 55415 17.1701 . . ID=Chr1:SNP:55415;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 55460 55460 17.1701 . . ID=Chr1:SNP:55460;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 55491 55491 17.1701 . . ID=Chr1:SNP:55491;Variant_seq=CC;Reference_seq=AA;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 55917 55917 17.1701 . . ID=Chr1:SNP:55917;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 56372 56372 4.77465 . . ID=Chr1:SNP:56372;Variant_seq=T;Reference_seq=G;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 56383 56383 2.50735 . . ID=Chr1:SNP:56383;Variant_seq=T;Reference_seq=G;Total_reads=3;Zygosity=3:HET +Chr1 SAMTOOLS SNP 56399 56399 4.77465 . . ID=Chr1:SNP:56399;Variant_seq=C;Reference_seq=A;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 56430 56430 4.77465 . . ID=Chr1:SNP:56430;Variant_seq=C;Reference_seq=A;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 56448 56448 4.77465 . . ID=Chr1:SNP:56448;Variant_seq=G;Reference_seq=C;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 56477 56477 17.1701 . . ID=Chr1:SNP:56477;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 56586 56586 17.1701 . . ID=Chr1:SNP:56586;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 56642 56642 17.1701 . . ID=Chr1:SNP:56642;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 56672 56672 46.0861 . . ID=Chr1:SNP:56672;Variant_seq=TA;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 56708 56708 17.1701 . . ID=Chr1:SNP:56708;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 56728 56728 17.1701 . . ID=Chr1:SNP:56728;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 56743 56743 17.1701 . . ID=Chr1:SNP:56743;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 56750 56750 1.76687 . . ID=Chr1:SNP:56750;Variant_seq=C;Reference_seq=G;Total_reads=4;Zygosity=4:HET +Chr1 SAMTOOLS SNP 56756 56756 1.76687 . . ID=Chr1:SNP:56756;Variant_seq=T;Reference_seq=A;Total_reads=4;Zygosity=4:HET +Chr1 SAMTOOLS SNP 56769 56769 1.76687 . . ID=Chr1:SNP:56769;Variant_seq=T;Reference_seq=A;Total_reads=4;Zygosity=4:HET +Chr1 SAMTOOLS SNP 56792 56792 1.76687 . . ID=Chr1:SNP:56792;Variant_seq=T;Reference_seq=A;Total_reads=4;Zygosity=4:HET +Chr1 SAMTOOLS SNP 56800 56800 1.76687 . . ID=Chr1:SNP:56800;Variant_seq=T;Reference_seq=A;Total_reads=4;Zygosity=4:HET +Chr1 SAMTOOLS SNP 56803 56803 1.76687 . . ID=Chr1:SNP:56803;Variant_seq=G;Reference_seq=C;Total_reads=4;Zygosity=4:HET +Chr1 SAMTOOLS SNP 56822 56822 2.50735 . . ID=Chr1:SNP:56822;Variant_seq=T;Reference_seq=A;Total_reads=3;Zygosity=3:HET +Chr1 SAMTOOLS SNP 57075 57075 4.77465 . . ID=Chr1:SNP:57075;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 57129 57129 4.77465 . . ID=Chr1:SNP:57129;Variant_seq=T;Reference_seq=A;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 57130 57130 4.77465 . . ID=Chr1:SNP:57130;Variant_seq=T;Reference_seq=A;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 57164 57164 17.1701 . . ID=Chr1:SNP:57164;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 57166 57166 17.1701 . . ID=Chr1:SNP:57166;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 57533 57533 17.1701 . . ID=Chr1:SNP:57533;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 57543 57543 17.1701 . . ID=Chr1:SNP:57543;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 57561 57561 17.1701 . . ID=Chr1:SNP:57561;Variant_seq=ATCGC;Reference_seq=TTCGA;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 57885 57885 17.1701 . . ID=Chr1:SNP:57885;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 57929 57929 17.1701 . . ID=Chr1:SNP:57929;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 58372 58372 17.1701 . . ID=Chr1:SNP:58372;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 58383 58383 17.1701 . . ID=Chr1:SNP:58383;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 58391 58391 17.1701 . . ID=Chr1:SNP:58391;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 58399 58399 17.1701 . . ID=Chr1:SNP:58399;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 58807 58807 17.1701 . . ID=Chr1:SNP:58807;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 58825 58825 17.1701 . . ID=Chr1:SNP:58825;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 58844 58844 17.1701 . . ID=Chr1:SNP:58844;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 58862 58862 4.77465 . . ID=Chr1:SNP:58862;Variant_seq=T;Reference_seq=A;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 59508 59508 17.1701 . . ID=Chr1:SNP:59508;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 59524 59524 17.1701 . . ID=Chr1:SNP:59524;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 59546 59546 17.1701 . . ID=Chr1:SNP:59546;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 59554 59554 46.0861 . . ID=Chr1:SNP:59554;Variant_seq=CG;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 61378 61378 17.1701 . . ID=Chr1:SNP:61378;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 61387 61387 17.1701 . . ID=Chr1:SNP:61387;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 61599 61599 17.1701 . . ID=Chr1:SNP:61599;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 61652 61652 17.1701 . . ID=Chr1:SNP:61652;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 61882 61882 17.1701 . . ID=Chr1:SNP:61882;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 61904 61904 17.1701 . . ID=Chr1:SNP:61904;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 61913 61913 17.1701 . . ID=Chr1:SNP:61913;Variant_seq=TGC;Reference_seq=AGG;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 61957 61957 17.1701 . . ID=Chr1:SNP:61957;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 62010 62010 17.1701 . . ID=Chr1:SNP:62010;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 62056 62056 4.77465 . . ID=Chr1:SNP:62056;Variant_seq=A;Reference_seq=T;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 62168 62168 17.1701 . . ID=Chr1:SNP:62168;Variant_seq=GCGCG;Reference_seq=CCGCC;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 62290 62290 17.1701 . . ID=Chr1:SNP:62290;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 62446 62446 2.50735 . . ID=Chr1:SNP:62446;Variant_seq=G;Reference_seq=C;Total_reads=3;Zygosity=3:HET +Chr1 SAMTOOLS SNP 62447 62447 2.50735 . . ID=Chr1:SNP:62447;Variant_seq=ATAC;Reference_seq=CTAG;Total_reads=3;Zygosity=3:HET +Chr1 SAMTOOLS SNP 62462 62462 2.50735 . . ID=Chr1:SNP:62462;Variant_seq=G;Reference_seq=C;Total_reads=3;Zygosity=3:HET +Chr1 SAMTOOLS SNP 62478 62478 2.50735 . . ID=Chr1:SNP:62478;Variant_seq=G;Reference_seq=C;Total_reads=3;Zygosity=3:HET +Chr1 SAMTOOLS SNP 62514 62514 4.77465 . . ID=Chr1:SNP:62514;Variant_seq=T;Reference_seq=G;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 62598 62598 17.1701 . . ID=Chr1:SNP:62598;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 62634 62634 4.77465 . . ID=Chr1:SNP:62634;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 62658 62658 2.50735 . . ID=Chr1:SNP:62658;Variant_seq=G;Reference_seq=T;Total_reads=3;Zygosity=3:HET +Chr1 SAMTOOLS SNP 62665 62665 2.50735 . . ID=Chr1:SNP:62665;Variant_seq=C;Reference_seq=G;Total_reads=3;Zygosity=3:HET +Chr1 SAMTOOLS SNP 62686 62686 4.77465 . . ID=Chr1:SNP:62686;Variant_seq=T;Reference_seq=A;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 62697 62697 4.77465 . . ID=Chr1:SNP:62697;Variant_seq=A;Reference_seq=C;Total_reads=2;Zygosity=2:HET +Chr1 SAMTOOLS SNP 62758 62758 17.1701 . . ID=Chr1:SNP:62758;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 62769 62769 17.1701 . . ID=Chr1:SNP:62769;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 62841 62841 17.1701 . . ID=Chr1:SNP:62841;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 62852 62852 17.1701 . . ID=Chr1:SNP:62852;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 62929 62929 17.1701 . . ID=Chr1:SNP:62929;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 63049 63049 17.1701 . . ID=Chr1:SNP:63049;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut +Chr1 SAMTOOLS SNP 63120 63120 4.77465 . . ID=Chr1:SNP:63120;Variant_seq=A;Reference_seq=C;Total_reads=2;Zygosity=2:HET
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ipcress.out Thu May 22 20:30:19 2014 -0400 @@ -0,0 +1,341 @@ + +Ipcress result +-------------- + Experiment: k69_93535:SAMTOOLS:SNP:1147 + Primers: A B + Target: k69_93535:filter(unmasked) + Matches: 20/20 23/23 + Product: 83 bp (range 50-100) +Result type: forward + +...GGACAGGGAAGCTTCATAGG................................. # forward + ||||||||||||||||||||--> +5'-GGACAGGGAAGCTTCATAGG-3' 3'-CTCCTAAACTAGAAAGTCCAAAC-5' # primers + <--||||||||||||||||||||||| +..............................CTCCTAAACTAGAAAGTCCAAAC... # revcomp +-- +ipcress: k69_93535:filter(unmasked) k69_93535:SAMTOOLS:SNP:1147 83 A 1088 0 B 1148 0 forward + +Ipcress result +-------------- + Experiment: k69_93535:SAMTOOLS:SNP:1147 + Primers: A B + Target: k69_93535:filter(unmasked) + Matches: 21/21 21/21 + Product: 86 bp (range 50-100) +Result type: forward + +...CTTTGAGTCTGAACGCATTTG............................... # forward + |||||||||||||||||||||--> +5'-CTTTGAGTCTGAACGCATTTG-3' 3'-CTTCTTTGCCCTCTACTTTGT-5' # primers + <--||||||||||||||||||||| +...............................CTTCTTTGCCCTCTACTTTGT... # revcomp +-- +ipcress: k69_93535:filter(unmasked) k69_93535:SAMTOOLS:SNP:1147 86 A 1109 0 B 1174 0 forward + +Ipcress result +-------------- + Experiment: k69_93535:SAMTOOLS:SNP:1147 + Primers: A B + Target: k69_93535:filter(unmasked) + Matches: 20/20 20/20 + Product: 87 bp (range 50-100) +Result type: forward + +...TTTGAGTCTGAACGCATTTG.............................. # forward + ||||||||||||||||||||--> +5'-TTTGAGTCTGAACGCATTTG-3' 3'-CTTTGCCCTCTACTTTGTTC-5' # primers + <--|||||||||||||||||||| +..............................CTTTGCCCTCTACTTTGTTC... # revcomp +-- +ipcress: k69_93535:filter(unmasked) k69_93535:SAMTOOLS:SNP:1147 87 A 1110 0 B 1177 0 forward + +Ipcress result +-------------- + Experiment: k69_93535:SAMTOOLS:SNP:1147 + Primers: A B + Target: k69_93535:filter(unmasked) + Matches: 21/21 21/21 + Product: 89 bp (range 50-100) +Result type: forward + +...CTTTGAGTCTGAACGCATTTG............................... # forward + |||||||||||||||||||||--> +5'-CTTTGAGTCTGAACGCATTTG-3' 3'-CTTTGCCCTCTACTTTGTTCT-5' # primers + <--||||||||||||||||||||| +...............................CTTTGCCCTCTACTTTGTTCT... # revcomp +-- +ipcress: k69_93535:filter(unmasked) k69_93535:SAMTOOLS:SNP:1147 89 A 1109 0 B 1177 0 forward + +Ipcress result +-------------- + Experiment: k69_93535:SAMTOOLS:SNP:1147 + Primers: A B + Target: k69_93535:filter(unmasked) + Matches: 21/21 21/21 + Product: 93 bp (range 50-100) +Result type: forward + +...CTTTGAGTCTGAACGCATTTG............................... # forward + |||||||||||||||||||||--> +5'-CTTTGAGTCTGAACGCATTTG-3' 3'-GCCCTCTACTTTGTTCTAAAC-5' # primers + <--||||||||||||||||||||| +...............................GCCCTCTACTTTGTTCTAAAC... # revcomp +-- +ipcress: k69_93535:filter(unmasked) k69_93535:SAMTOOLS:SNP:1147 93 A 1109 0 B 1181 0 forward + +Ipcress result +-------------- + Experiment: k69_93535:SAMTOOLS:SNP:1336 + Primers: A B + Target: k69_93535:filter(unmasked) + Matches: 20/20 22/22 + Product: 82 bp (range 50-100) +Result type: forward + +...TTAGAAGGAACGCGAGAAGG................................ # forward + ||||||||||||||||||||--> +5'-TTAGAAGGAACGCGAGAAGG-3' 3'-GAATGCGGATCAAACCAACAAC-5' # primers + <--|||||||||||||||||||||| +..............................GAATGCGGATCAAACCAACAAC... # revcomp +-- +ipcress: k69_93535:filter(unmasked) k69_93535:SAMTOOLS:SNP:1336 82 A 1297 0 B 1357 0 forward + +Ipcress result +-------------- + Experiment: k69_93535:SAMTOOLS:SNP:1336 + Primers: A B + Target: k69_93535:filter(unmasked) + Matches: 20/20 20/20 + Product: 85 bp (range 50-100) +Result type: forward + +...TTTAGAAGGAACGCGAGAAG.............................. # forward + ||||||||||||||||||||--> +5'-TTTAGAAGGAACGCGAGAAG-3' 3'-GCGGATCAAACCAACAACAA-5' # primers + <--|||||||||||||||||||| +..............................GCGGATCAAACCAACAACAA... # revcomp +-- +ipcress: k69_93535:filter(unmasked) k69_93535:SAMTOOLS:SNP:1336 85 A 1296 0 B 1361 0 forward + +Ipcress result +-------------- + Experiment: k69_93535:SAMTOOLS:SNP:1336 + Primers: A B + Target: k69_93535:filter(unmasked) + Matches: 21/21 20/20 + Product: 86 bp (range 50-100) +Result type: forward + +...GTTTAGAAGGAACGCGAGAAG.............................. # forward + |||||||||||||||||||||--> +5'-GTTTAGAAGGAACGCGAGAAG-3' 3'-GCGGATCAAACCAACAACAA-5' # primers + <--|||||||||||||||||||| +...............................GCGGATCAAACCAACAACAA... # revcomp +-- +ipcress: k69_93535:filter(unmasked) k69_93535:SAMTOOLS:SNP:1336 86 A 1295 0 B 1361 0 forward + +Ipcress result +-------------- + Experiment: k69_93535:SAMTOOLS:SNP:1336 + Primers: A B + Target: k69_93535:filter(unmasked) + Matches: 20/20 22/22 + Product: 87 bp (range 50-100) +Result type: forward + +...TTAGAAGGAACGCGAGAAGG................................ # forward + ||||||||||||||||||||--> +5'-TTAGAAGGAACGCGAGAAGG-3' 3'-CGGATCAAACCAACAACAACTC-5' # primers + <--|||||||||||||||||||||| +..............................CGGATCAAACCAACAACAACTC... # revcomp +-- +ipcress: k69_93535:filter(unmasked) k69_93535:SAMTOOLS:SNP:1336 87 A 1297 0 B 1362 0 forward + +Ipcress result +-------------- + Experiment: k69_93535:SAMTOOLS:SNP:1336 + Primers: A B + Target: k69_93535:filter(unmasked) + Matches: 20/20 22/22 + Product: 88 bp (range 50-100) +Result type: forward + +...TTAGAAGGAACGCGAGAAGG................................ # forward + ||||||||||||||||||||--> +5'-TTAGAAGGAACGCGAGAAGG-3' 3'-GGATCAAACCAACAACAACTCG-5' # primers + <--|||||||||||||||||||||| +..............................GGATCAAACCAACAACAACTCG... # revcomp +-- +ipcress: k69_93535:filter(unmasked) k69_93535:SAMTOOLS:SNP:1336 88 A 1297 0 B 1363 0 forward + +Ipcress result +-------------- + Experiment: k69_98089:SAMTOOLS:SNP:30 + Primers: A B + Target: k69_98089:filter(unmasked) + Matches: 25/25 19/19 + Product: 88 bp (range 50-100) +Result type: forward + +...CAAATCCAAACATGTTATCTTCTTC............................. # forward + |||||||||||||||||||||||||--> +5'-CAAATCCAAACATGTTATCTTCTTC-3' 3'-GCGAGTTGCAGTCTAGTAG-5' # primers + <--||||||||||||||||||| +...................................GCGAGTTGCAGTCTAGTAG... # revcomp +-- +ipcress: k69_98089:filter(unmasked) k69_98089:SAMTOOLS:SNP:30 88 A 1 0 B 70 0 forward + +Ipcress result +-------------- + Experiment: k69_98089:SAMTOOLS:SNP:30 + Primers: A B + Target: k69_98089:filter(unmasked) + Matches: 25/25 20/20 + Product: 90 bp (range 50-100) +Result type: forward + +...CAAATCCAAACATGTTATCTTCTTC.............................. # forward + |||||||||||||||||||||||||--> +5'-CAAATCCAAACATGTTATCTTCTTC-3' 3'-CGAGTTGCAGTCTAGTAGTT-5' # primers + <--|||||||||||||||||||| +...................................CGAGTTGCAGTCTAGTAGTT... # revcomp +-- +ipcress: k69_98089:filter(unmasked) k69_98089:SAMTOOLS:SNP:30 90 A 1 0 B 71 0 forward + +Ipcress result +-------------- + Experiment: k69_98089:SAMTOOLS:SNP:30 + Primers: A B + Target: k69_98089:filter(unmasked) + Matches: 25/25 21/21 + Product: 91 bp (range 50-100) +Result type: forward + +...CAAATCCAAACATGTTATCTTCTTC............................... # forward + |||||||||||||||||||||||||--> +5'-CAAATCCAAACATGTTATCTTCTTC-3' 3'-CGAGTTGCAGTCTAGTAGTTG-5' # primers + <--||||||||||||||||||||| +...................................CGAGTTGCAGTCTAGTAGTTG... # revcomp +-- +ipcress: k69_98089:filter(unmasked) k69_98089:SAMTOOLS:SNP:30 91 A 1 0 B 71 0 forward + +Ipcress result +-------------- + Experiment: k69_98089:SAMTOOLS:SNP:30 + Primers: A B + Target: k69_98089:filter(unmasked) + Matches: 25/25 20/20 + Product: 96 bp (range 50-100) +Result type: forward + +...CAAATCCAAACATGTTATCTTCTTC.............................. # forward + |||||||||||||||||||||||||--> +5'-CAAATCCAAACATGTTATCTTCTTC-3' 3'-GCAGTCTAGTAGTTGTGCTT-5' # primers + <--|||||||||||||||||||| +...................................GCAGTCTAGTAGTTGTGCTT... # revcomp +-- +ipcress: k69_98089:filter(unmasked) k69_98089:SAMTOOLS:SNP:30 96 A 1 0 B 77 0 forward + +Ipcress result +-------------- + Experiment: k69_98089:SAMTOOLS:SNP:30 + Primers: A B + Target: k69_98089:filter(unmasked) + Matches: 25/25 21/21 + Product: 97 bp (range 50-100) +Result type: forward + +...CAAATCCAAACATGTTATCTTCTTC............................... # forward + |||||||||||||||||||||||||--> +5'-CAAATCCAAACATGTTATCTTCTTC-3' 3'-GCAGTCTAGTAGTTGTGCTTG-5' # primers + <--||||||||||||||||||||| +...................................GCAGTCTAGTAGTTGTGCTTG... # revcomp +-- +ipcress: k69_98089:filter(unmasked) k69_98089:SAMTOOLS:SNP:30 97 A 1 0 B 77 0 forward + +Ipcress result +-------------- + Experiment: k69_98089:SAMTOOLS:SNP:550 + Primers: A B + Target: k69_98089:filter(unmasked) + Matches: 22/22 24/24 + Product: 88 bp (range 50-100) +Result type: forward + +...TGAATTGATACTGAAATTCGGG.................................. # forward + ||||||||||||||||||||||--> +5'-TGAATTGATACTGAAATTCGGG-3' 3'-CTAACACCTTTGAAAGTACATACG-5' # primers + <--|||||||||||||||||||||||| +................................CTAACACCTTTGAAAGTACATACG... # revcomp +-- +ipcress: k69_98089:filter(unmasked) k69_98089:SAMTOOLS:SNP:550 88 A 499 0 B 563 0 forward + +Ipcress result +-------------- + Experiment: k69_98089:SAMTOOLS:SNP:550 + Primers: A B + Target: k69_98089:filter(unmasked) + Matches: 22/22 24/24 + Product: 77 bp (range 50-100) +Result type: forward + +...TGAAATTCGGGAAGACTGAAAG.................................. # forward + ||||||||||||||||||||||--> +5'-TGAAATTCGGGAAGACTGAAAG-3' 3'-CTAACACCTTTGAAAGTACATACG-5' # primers + <--|||||||||||||||||||||||| +................................CTAACACCTTTGAAAGTACATACG... # revcomp +-- +ipcress: k69_98089:filter(unmasked) k69_98089:SAMTOOLS:SNP:550 77 A 510 0 B 563 0 forward + +Ipcress result +-------------- + Experiment: k69_98089:SAMTOOLS:SNP:550 + Primers: A B + Target: k69_98089:filter(unmasked) + Matches: 19/19 25/25 + Product: 75 bp (range 50-100) +Result type: forward + +...CGGGAAGACTGAAAGAACG................................... # forward + |||||||||||||||||||--> +5'-CGGGAAGACTGAAAGAACG-3' 3'-CACCTTTGAAAGTACATACGATAGA-5' # primers + <--||||||||||||||||||||||||| +.............................CACCTTTGAAAGTACATACGATAGA... # revcomp +-- +ipcress: k69_98089:filter(unmasked) k69_98089:SAMTOOLS:SNP:550 75 A 517 0 B 567 0 forward + +Ipcress result +-------------- + Experiment: k69_98089:SAMTOOLS:SNP:550 + Primers: A B + Target: k69_98089:filter(unmasked) + Matches: 21/21 25/25 + Product: 81 bp (range 50-100) +Result type: forward + +...GAAATTCGGGAAGACTGAAAG................................... # forward + |||||||||||||||||||||--> +5'-GAAATTCGGGAAGACTGAAAG-3' 3'-CACCTTTGAAAGTACATACGATAGA-5' # primers + <--||||||||||||||||||||||||| +...............................CACCTTTGAAAGTACATACGATAGA... # revcomp +-- +ipcress: k69_98089:filter(unmasked) k69_98089:SAMTOOLS:SNP:550 81 A 511 0 B 567 0 forward + +Ipcress result +-------------- + Experiment: k69_98089:SAMTOOLS:SNP:550 + Primers: A B + Target: k69_98089:filter(unmasked) + Matches: 22/22 25/25 + Product: 79 bp (range 50-100) +Result type: forward + +...AATTCGGGAAGACTGAAAGAAC................................... # forward + ||||||||||||||||||||||--> +5'-AATTCGGGAAGACTGAAAGAAC-3' 3'-CACCTTTGAAAGTACATACGATAGA-5' # primers + <--||||||||||||||||||||||||| +................................CACCTTTGAAAGTACATACGATAGA... # revcomp +-- +ipcress: k69_98089:filter(unmasked) k69_98089:SAMTOOLS:SNP:550 79 A 513 0 B 567 0 forward +-- completed ipcress analysis
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ipcress_gff.out Thu May 22 20:30:19 2014 -0400 @@ -0,0 +1,20 @@ +k69_93535 ipcress PCR_product 1088 1148 . + . Name=k69_93535:SAMTOOLS:SNP:1147 +k69_93535 ipcress PCR_product 1109 1174 . + . Name=k69_93535:SAMTOOLS:SNP:1147 +k69_93535 ipcress PCR_product 1110 1177 . + . Name=k69_93535:SAMTOOLS:SNP:1147 +k69_93535 ipcress PCR_product 1109 1177 . + . Name=k69_93535:SAMTOOLS:SNP:1147 +k69_93535 ipcress PCR_product 1109 1181 . + . Name=k69_93535:SAMTOOLS:SNP:1147 +k69_93535 ipcress PCR_product 1297 1357 . + . Name=k69_93535:SAMTOOLS:SNP:1336 +k69_93535 ipcress PCR_product 1296 1361 . + . Name=k69_93535:SAMTOOLS:SNP:1336 +k69_93535 ipcress PCR_product 1295 1361 . + . Name=k69_93535:SAMTOOLS:SNP:1336 +k69_93535 ipcress PCR_product 1297 1362 . + . Name=k69_93535:SAMTOOLS:SNP:1336 +k69_93535 ipcress PCR_product 1297 1363 . + . Name=k69_93535:SAMTOOLS:SNP:1336 +k69_98089 ipcress PCR_product 1 70 . + . Name=k69_98089:SAMTOOLS:SNP:30 +k69_98089 ipcress PCR_product 1 71 . + . Name=k69_98089:SAMTOOLS:SNP:30 +k69_98089 ipcress PCR_product 1 71 . + . Name=k69_98089:SAMTOOLS:SNP:30 +k69_98089 ipcress PCR_product 1 77 . + . Name=k69_98089:SAMTOOLS:SNP:30 +k69_98089 ipcress PCR_product 1 77 . + . Name=k69_98089:SAMTOOLS:SNP:30 +k69_98089 ipcress PCR_product 499 563 . + . Name=k69_98089:SAMTOOLS:SNP:550 +k69_98089 ipcress PCR_product 510 563 . + . Name=k69_98089:SAMTOOLS:SNP:550 +k69_98089 ipcress PCR_product 517 567 . + . Name=k69_98089:SAMTOOLS:SNP:550 +k69_98089 ipcress PCR_product 511 567 . + . Name=k69_98089:SAMTOOLS:SNP:550 +k69_98089 ipcress PCR_product 513 567 . + . Name=k69_98089:SAMTOOLS:SNP:550
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ipcress_test_input.txt Thu May 22 20:30:19 2014 -0400 @@ -0,0 +1,20 @@ +k69_93535:SAMTOOLS:SNP:1147 CTTTGAGTCTGAACGCATTTG TGTTTCATCTCCCGTTTCTTC +k69_93535:SAMTOOLS:SNP:1147 CTTTGAGTCTGAACGCATTTG TCTTGTTTCATCTCCCGTTTC +k69_93535:SAMTOOLS:SNP:1147 CTTTGAGTCTGAACGCATTTG CAAATCTTGTTTCATCTCCCG +k69_93535:SAMTOOLS:SNP:1147 TTTGAGTCTGAACGCATTTG CTTGTTTCATCTCCCGTTTC +k69_93535:SAMTOOLS:SNP:1147 GGACAGGGAAGCTTCATAGG CAAACCTGAAAGATCAAATCCTC +k69_93535:SAMTOOLS:SNP:1336 TTAGAAGGAACGCGAGAAGG CAACAACCAAACTAGGCGTAAG +k69_93535:SAMTOOLS:SNP:1336 TTAGAAGGAACGCGAGAAGG CTCAACAACAACCAAACTAGGC +k69_93535:SAMTOOLS:SNP:1336 TTAGAAGGAACGCGAGAAGG GCTCAACAACAACCAAACTAGG +k69_93535:SAMTOOLS:SNP:1336 TTTAGAAGGAACGCGAGAAG AACAACAACCAAACTAGGCG +k69_93535:SAMTOOLS:SNP:1336 GTTTAGAAGGAACGCGAGAAG AACAACAACCAAACTAGGCG +k69_98089:SAMTOOLS:SNP:30 CAAATCCAAACATGTTATCTTCTTC TTCGTGTTGATGATCTGACG +k69_98089:SAMTOOLS:SNP:30 CAAATCCAAACATGTTATCTTCTTC GTTCGTGTTGATGATCTGACG +k69_98089:SAMTOOLS:SNP:30 CAAATCCAAACATGTTATCTTCTTC TTGATGATCTGACGTTGAGC +k69_98089:SAMTOOLS:SNP:30 CAAATCCAAACATGTTATCTTCTTC GTTGATGATCTGACGTTGAGC +k69_98089:SAMTOOLS:SNP:30 CAAATCCAAACATGTTATCTTCTTC GATGATCTGACGTTGAGCG +k69_98089:SAMTOOLS:SNP:550 TGAATTGATACTGAAATTCGGG GCATACATGAAAGTTTCCACAATC +k69_98089:SAMTOOLS:SNP:550 CGGGAAGACTGAAAGAACG AGATAGCATACATGAAAGTTTCCAC +k69_98089:SAMTOOLS:SNP:550 GAAATTCGGGAAGACTGAAAG AGATAGCATACATGAAAGTTTCCAC +k69_98089:SAMTOOLS:SNP:550 AATTCGGGAAGACTGAAAGAAC AGATAGCATACATGAAAGTTTCCAC +k69_98089:SAMTOOLS:SNP:550 TGAAATTCGGGAAGACTGAAAG GCATACATGAAAGTTTCCACAATC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mpileup_out.vcf Thu May 22 20:30:19 2014 -0400 @@ -0,0 +1,500 @@ +##fileformat=VCFv4.1 +##samtoolsVersion=0.1.19-44428cd +##reference=file:///tmp/tmp-SAMTOOLS-zkHTpr/reference_input.fa +##contig=<ID=Chr1,length=17971566> +##contig=<ID=Chr10,length=15490421> +##contig=<ID=Chr11,length=17082262> +##contig=<ID=Chr12,length=13002763> +##contig=<ID=Chr13,length=17372821> +##contig=<ID=Chr14,length=12031045> +##contig=<ID=Chr15,length=19001909> +##contig=<ID=Chr16,length=11476499> +##contig=<ID=Chr17,length=14675105> +##contig=<ID=Chr18,length=14814751> +##contig=<ID=Chr19,length=11145676> +##contig=<ID=Chr2,length=15003700> +##contig=<ID=Chr20,length=14375345> +##contig=<ID=Chr21,length=14287830> +##contig=<ID=Chr22,length=12982530> +##contig=<ID=Chr23,length=20688064> +##contig=<ID=Chr24,length=17702303> +##contig=<ID=Chr25,length=14321294> +##contig=<ID=Chr26,length=17153587> +##contig=<ID=Chr27,length=10917718> +##contig=<ID=Chr28,length=16406049> +##contig=<ID=Chr29,length=14180785> +##contig=<ID=Chr3,length=20519224> +##contig=<ID=Chr4,length=13065296> +##contig=<ID=Chr5,length=18825850> +##contig=<ID=Chr6,length=18208465> +##contig=<ID=Chr7,length=18704015> +##contig=<ID=Chr8,length=21083321> +##contig=<ID=Chr9,length=11598160> +##contig=<ID=Unknow,length=177361715> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth"> +##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases"> +##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads"> +##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same"> +##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele frequency (assuming HWE)"> +##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)"> +##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> +##INFO=<ID=IS,Number=2,Type=Float,Description="Maximum number of reads supporting an indel and fraction of indel reads"> +##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes for each ALT allele, in the same order as listed"> +##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies"> +##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3"> +##INFO=<ID=CLR,Number=1,Type=Integer,Description="Log ratio of genotype likelihoods with and without the constraint"> +##INFO=<ID=UGT,Number=1,Type=String,Description="The most probable unconstrained genotype configuration in the trio"> +##INFO=<ID=CGT,Number=1,Type=String,Description="The most probable constrained genotype configuration in the trio"> +##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias"> +##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> +##INFO=<ID=PC2,Number=2,Type=Integer,Description="Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in group2."> +##INFO=<ID=PCHI2,Number=1,Type=Float,Description="Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples."> +##INFO=<ID=QCHI2,Number=1,Type=Integer,Description="Phred scaled PCHI2."> +##INFO=<ID=PR,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2."> +##INFO=<ID=QBD,Number=1,Type=Float,Description="Quality by Depth: QUAL/#reads"> +##INFO=<ID=RPB,Number=1,Type=Float,Description="Read Position Bias"> +##INFO=<ID=MDV,Number=1,Type=Integer,Description="Maximum number of high-quality nonRef reads in samples"> +##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias (v2) for filtering splice-site artefacts in RNA-seq data. Note: this version may be broken."> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> +##FORMAT=<ID=GL,Number=3,Type=Float,Description="Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases"> +##FORMAT=<ID=DV,Number=1,Type=Integer,Description="# high-quality non-reference bases"> +##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value"> +##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT /tmp/tmp-SAMTOOLS-zkHTpr/bam_input_0.bam +Chr1 14086 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14087 . A . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4 PL 4 +Chr1 14088 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14089 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14090 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14091 . A . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4 PL 4 +Chr1 14092 . A . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4 PL 4 +Chr1 14093 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14094 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14095 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14096 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14097 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14098 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14099 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14100 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14101 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14102 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14103 . A . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4 PL 4 +Chr1 14104 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14105 . T . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4 PL 4 +Chr1 14106 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14107 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14108 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14109 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14110 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14111 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14112 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14113 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14114 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14115 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14116 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14117 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14118 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14119 . A . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4 PL 4 +Chr1 14120 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14121 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14122 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14123 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14124 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14125 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14126 . A . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4 PL 4 +Chr1 14127 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14128 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14129 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14130 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14131 . G . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4 PL 4 +Chr1 14132 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14133 . A . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4 PL 4 +Chr1 14134 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14135 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14136 . G . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4 PL 4 +Chr1 14137 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14138 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14139 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14140 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14141 . T . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4 PL 4 +Chr1 14142 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14143 . A . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4 PL 4 +Chr1 14144 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14145 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14146 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14147 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14148 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14149 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14150 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14151 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14152 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14153 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14154 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14155 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14156 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14157 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14158 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14159 . G . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4 PL 4 +Chr1 14160 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14161 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14162 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14163 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14164 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14165 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14166 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14167 . A . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4 PL 4 +Chr1 14168 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14169 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14170 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14171 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14172 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14173 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14174 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14175 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14176 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14177 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14178 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14179 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14180 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14181 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14182 . T . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4 PL 4 +Chr1 14183 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14184 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14185 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14230 . G . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4 PL 4 +Chr1 14231 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14232 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14233 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14234 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14235 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14236 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14237 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14238 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14239 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14240 . C . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4 PL 4 +Chr1 14241 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14242 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14243 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14244 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14245 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14246 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14247 . G . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4 PL 4 +Chr1 14248 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14249 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14250 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14251 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14252 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14253 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14254 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14255 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14256 . A . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4 PL 4 +Chr1 14257 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14258 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14259 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14260 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14261 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14262 . T . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4 PL 4 +Chr1 14263 . T . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4 PL 4 +Chr1 14264 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14265 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14266 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14267 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14268 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14269 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14270 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14271 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14272 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14273 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14274 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14275 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14276 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14277 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14278 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14279 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14280 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14281 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14282 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14283 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14284 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14285 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14286 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14287 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14288 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14289 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14290 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14291 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14292 . T . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4 PL 4 +Chr1 14293 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14294 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14295 . G . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4 PL 4 +Chr1 14296 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14297 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14298 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14299 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14300 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14301 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14302 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14303 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14304 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14305 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14306 . A . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4 PL 4 +Chr1 14307 . C . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4 PL 4 +Chr1 14308 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14309 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14310 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14311 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14312 . C . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4 PL 4 +Chr1 14313 . G . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4 PL 4 +Chr1 14314 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14315 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14316 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14317 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14318 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14319 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14320 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14320 . TC . 33.5 . INDEL;IS=1,1.000000;DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-39 PL 4 +Chr1 14321 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14322 . T . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4 PL 4 +Chr1 14323 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14324 . T . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4 PL 4 +Chr1 14325 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14326 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 14327 . A . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4 PL 4 +Chr1 14328 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120479 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120480 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120481 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120482 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120483 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120484 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120485 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120486 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120487 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120488 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120489 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120490 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120491 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120492 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120493 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120494 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120495 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120496 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120497 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120498 . C . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4 PL 4 +Chr1 120499 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120500 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120501 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120502 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120503 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120504 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120505 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120506 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120507 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120508 . G . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4 PL 4 +Chr1 120509 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120510 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120511 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120512 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120513 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120514 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120515 . A . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4 PL 4 +Chr1 120516 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120517 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120518 . C . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4 PL 4 +Chr1 120519 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120520 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120521 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120522 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120523 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120524 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120525 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120526 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120527 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120528 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120529 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120530 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120531 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120532 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120533 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120534 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120535 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120536 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120537 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120538 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120539 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120540 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120541 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120542 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120543 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120544 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120545 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120546 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120547 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120548 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120549 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120550 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120551 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120552 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120553 . C . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4 PL 4 +Chr1 120554 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120555 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120556 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120557 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120558 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120559 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120560 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120561 . G . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4 PL 4 +Chr1 120562 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120563 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120564 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120565 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120566 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120567 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120568 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120569 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120570 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120571 . A . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4 PL 4 +Chr1 120572 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120573 . G . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4 PL 4 +Chr1 120574 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120575 . T . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4 PL 4 +Chr1 120576 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120577 . A . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4 PL 4 +Chr1 120578 . C . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=0;FQ=-31.4 PL 4 +Chr1 120594 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120595 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120596 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120597 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120598 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120599 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120600 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120601 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120602 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120603 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120604 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120605 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120606 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120607 . A . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4 PL 4 +Chr1 120608 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120609 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120610 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120611 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120612 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120613 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120614 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120615 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120616 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120617 . T . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4 PL 4 +Chr1 120618 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120619 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120620 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120621 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120622 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120623 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120624 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120625 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120626 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120627 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120628 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120629 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120630 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120631 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120632 . C . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4 PL 4 +Chr1 120633 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120634 . A . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4 PL 4 +Chr1 120635 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120636 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120637 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120638 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120639 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120640 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120641 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120642 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120643 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120644 . A . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4 PL 4 +Chr1 120645 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120646 . G . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4 PL 4 +Chr1 120647 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120648 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120649 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120650 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120651 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120652 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120653 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120654 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120655 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120656 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120657 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120658 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120659 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120660 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120661 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120662 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120663 . T . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4 PL 4 +Chr1 120664 . G . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4 PL 4 +Chr1 120665 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120666 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120667 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120668 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120669 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120670 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120671 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120672 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120673 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120674 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120675 . G . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4 PL 4 +Chr1 120676 . G . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4 PL 4 +Chr1 120677 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120678 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120679 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120680 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120681 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120682 . A . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4 PL 4 +Chr1 120683 . G . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4 PL 4 +Chr1 120684 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120685 . G . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4 PL 4 +Chr1 120686 . T . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4 PL 4 +Chr1 120687 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120688 . G . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4 PL 4 +Chr1 120689 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120690 . G . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4 PL 4 +Chr1 120691 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 120692 . G . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=0;FQ=-31.4 PL 4 +Chr1 120693 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=0;FQ=-31.4 PL 0 +Chr1 1072445 . A . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=8;FQ=-31.4 PL 4 +Chr1 1072446 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-31.4 PL 0 +Chr1 1072447 . C . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-31.4 PL 0 +Chr1 1072448 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-31.4 PL 0 +Chr1 1072449 . A . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=8;FQ=-31.4 PL 4 +Chr1 1072450 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-31.4 PL 0 +Chr1 1072451 . T . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=8;FQ=-31.4 PL 4 +Chr1 1072452 . T . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-31.4 PL 0 +Chr1 1072453 . G . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=8;FQ=-31.4 PL 4 +Chr1 1072454 . A . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=8;FQ=-31.4 PL 4 +Chr1 1072455 . G . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=8;FQ=-31.4 PL 4 +Chr1 1072456 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-31.4 PL 0 +Chr1 1072457 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-31.4 PL 0 +Chr1 1072458 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-31.4 PL 0 +Chr1 1072459 . T . 26 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=8;FQ=-31.4 PL 4 +Chr1 1072460 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-31.4 PL 0 +Chr1 1072461 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-31.4 PL 0 +Chr1 1072461 . A . 33.5 . INDEL;IS=1,1.000000;DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=8;FQ=-39 PL 4 +Chr1 1072462 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-31.4 PL 0 +Chr1 1072463 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-31.4 PL 0 +Chr1 1072464 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-31.4 PL 0 +Chr1 1072465 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-31.4 PL 0 +Chr1 1072466 . G . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-31.4 PL 0 +Chr1 1072467 . A . 32 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-31 PL 0 +Chr1 1072468 . G . 32.4 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-30.6 PL 0 +Chr1 1072469 . G . 32.4 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-30.6 PL 0 +Chr1 1072470 . A . 32.4 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-30.6 PL 0 +Chr1 1072471 . T . 32.4 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-30.6 PL 0 +Chr1 1072472 . C . 32.4 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-30.6 PL 0 +Chr1 1072473 . C . 32.4 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-30.6 PL 0 +Chr1 1072474 . A . 32.4 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-30.6 PL 0 +Chr1 1072475 . G . 32.4 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-30.6 PL 0 +Chr1 1072476 . T . 32.4 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-30.6 PL 0 +Chr1 1072477 . A . 32.4 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-30.6 PL 0 +Chr1 1072478 . A . 32.4 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=8;FQ=-30.6 PL 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mpileup_vcf_to_gff_output.gff Thu May 22 20:30:19 2014 -0400 @@ -0,0 +1,436 @@ +#gff-version 3 +Chr1 SAMTOOLS SNP 14086 14086 31.5 . . ID=Chr1:SNP:14086;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14087 14087 26 . . ID=Chr1:SNP:14087;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14088 14088 31.5 . . ID=Chr1:SNP:14088;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14089 14089 31.5 . . ID=Chr1:SNP:14089;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14090 14090 31.5 . . ID=Chr1:SNP:14090;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14091 14091 26 . . ID=Chr1:SNP:14091;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14092 14092 26 . . ID=Chr1:SNP:14092;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14093 14093 31.5 . . ID=Chr1:SNP:14093;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14094 14094 31.5 . . ID=Chr1:SNP:14094;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14095 14095 31.5 . . ID=Chr1:SNP:14095;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14096 14096 31.5 . . ID=Chr1:SNP:14096;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14097 14097 31.5 . . ID=Chr1:SNP:14097;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14098 14098 31.5 . . ID=Chr1:SNP:14098;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14099 14099 31.5 . . ID=Chr1:SNP:14099;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14100 14100 31.5 . . ID=Chr1:SNP:14100;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14101 14101 31.5 . . ID=Chr1:SNP:14101;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14102 14102 31.5 . . ID=Chr1:SNP:14102;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14103 14103 26 . . ID=Chr1:SNP:14103;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14104 14104 31.5 . . ID=Chr1:SNP:14104;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14105 14105 26 . . ID=Chr1:SNP:14105;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14106 14106 31.5 . . ID=Chr1:SNP:14106;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14107 14107 31.5 . . ID=Chr1:SNP:14107;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14108 14108 31.5 . . ID=Chr1:SNP:14108;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14109 14109 31.5 . . ID=Chr1:SNP:14109;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14110 14110 31.5 . . ID=Chr1:SNP:14110;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14111 14111 31.5 . . ID=Chr1:SNP:14111;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14112 14112 31.5 . . ID=Chr1:SNP:14112;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14113 14113 31.5 . . ID=Chr1:SNP:14113;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14114 14114 31.5 . . ID=Chr1:SNP:14114;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14115 14115 31.5 . . ID=Chr1:SNP:14115;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14116 14116 31.5 . . ID=Chr1:SNP:14116;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14117 14117 31.5 . . ID=Chr1:SNP:14117;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14118 14118 31.5 . . ID=Chr1:SNP:14118;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14119 14119 26 . . ID=Chr1:SNP:14119;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14120 14120 31.5 . . ID=Chr1:SNP:14120;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14121 14121 31.5 . . ID=Chr1:SNP:14121;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14122 14122 31.5 . . ID=Chr1:SNP:14122;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14123 14123 31.5 . . ID=Chr1:SNP:14123;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14124 14124 31.5 . . ID=Chr1:SNP:14124;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14125 14125 31.5 . . ID=Chr1:SNP:14125;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14126 14126 26 . . ID=Chr1:SNP:14126;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14127 14127 31.5 . . ID=Chr1:SNP:14127;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14128 14128 31.5 . . ID=Chr1:SNP:14128;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14129 14129 31.5 . . ID=Chr1:SNP:14129;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14130 14130 31.5 . . ID=Chr1:SNP:14130;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14131 14131 26 . . ID=Chr1:SNP:14131;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14132 14132 31.5 . . ID=Chr1:SNP:14132;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14133 14133 26 . . ID=Chr1:SNP:14133;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14134 14134 31.5 . . ID=Chr1:SNP:14134;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14135 14135 31.5 . . ID=Chr1:SNP:14135;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14136 14136 26 . . ID=Chr1:SNP:14136;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14137 14137 31.5 . . ID=Chr1:SNP:14137;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14138 14138 31.5 . . ID=Chr1:SNP:14138;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14139 14139 31.5 . . ID=Chr1:SNP:14139;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14140 14140 31.5 . . ID=Chr1:SNP:14140;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14141 14141 26 . . ID=Chr1:SNP:14141;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14142 14142 31.5 . . ID=Chr1:SNP:14142;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14143 14143 26 . . ID=Chr1:SNP:14143;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14144 14144 31.5 . . ID=Chr1:SNP:14144;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14145 14145 31.5 . . ID=Chr1:SNP:14145;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14146 14146 31.5 . . ID=Chr1:SNP:14146;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14147 14147 31.5 . . ID=Chr1:SNP:14147;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14148 14148 31.5 . . ID=Chr1:SNP:14148;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14149 14149 31.5 . . ID=Chr1:SNP:14149;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14150 14150 31.5 . . ID=Chr1:SNP:14150;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14151 14151 31.5 . . ID=Chr1:SNP:14151;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14152 14152 31.5 . . ID=Chr1:SNP:14152;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14153 14153 31.5 . . ID=Chr1:SNP:14153;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14154 14154 31.5 . . ID=Chr1:SNP:14154;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14155 14155 31.5 . . ID=Chr1:SNP:14155;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14156 14156 31.5 . . ID=Chr1:SNP:14156;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14157 14157 31.5 . . ID=Chr1:SNP:14157;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14158 14158 31.5 . . ID=Chr1:SNP:14158;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14159 14159 26 . . ID=Chr1:SNP:14159;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14160 14160 31.5 . . ID=Chr1:SNP:14160;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14161 14161 31.5 . . ID=Chr1:SNP:14161;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14162 14162 31.5 . . ID=Chr1:SNP:14162;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14163 14163 31.5 . . ID=Chr1:SNP:14163;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14164 14164 31.5 . . ID=Chr1:SNP:14164;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14165 14165 31.5 . . ID=Chr1:SNP:14165;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14166 14166 31.5 . . ID=Chr1:SNP:14166;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14167 14167 26 . . ID=Chr1:SNP:14167;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14168 14168 31.5 . . ID=Chr1:SNP:14168;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14169 14169 31.5 . . ID=Chr1:SNP:14169;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14170 14170 31.5 . . ID=Chr1:SNP:14170;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14171 14171 31.5 . . ID=Chr1:SNP:14171;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14172 14172 31.5 . . ID=Chr1:SNP:14172;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14173 14173 31.5 . . ID=Chr1:SNP:14173;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14174 14174 31.5 . . ID=Chr1:SNP:14174;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14175 14175 31.5 . . ID=Chr1:SNP:14175;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14176 14176 31.5 . . ID=Chr1:SNP:14176;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14177 14177 31.5 . . ID=Chr1:SNP:14177;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14178 14178 31.5 . . ID=Chr1:SNP:14178;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14179 14179 31.5 . . ID=Chr1:SNP:14179;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14180 14180 31.5 . . ID=Chr1:SNP:14180;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14181 14181 31.5 . . ID=Chr1:SNP:14181;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14182 14182 26 . . ID=Chr1:SNP:14182;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14183 14183 31.5 . . ID=Chr1:SNP:14183;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14184 14184 31.5 . . ID=Chr1:SNP:14184;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14185 14185 31.5 . . ID=Chr1:SNP:14185;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14230 14230 26 . . ID=Chr1:SNP:14230;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14231 14231 31.5 . . ID=Chr1:SNP:14231;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14232 14232 31.5 . . ID=Chr1:SNP:14232;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14233 14233 31.5 . . ID=Chr1:SNP:14233;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14234 14234 31.5 . . ID=Chr1:SNP:14234;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14235 14235 31.5 . . ID=Chr1:SNP:14235;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14236 14236 31.5 . . ID=Chr1:SNP:14236;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14237 14237 31.5 . . ID=Chr1:SNP:14237;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14238 14238 31.5 . . ID=Chr1:SNP:14238;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14239 14239 31.5 . . ID=Chr1:SNP:14239;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14240 14240 26 . . ID=Chr1:SNP:14240;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14241 14241 31.5 . . ID=Chr1:SNP:14241;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14242 14242 31.5 . . ID=Chr1:SNP:14242;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14243 14243 31.5 . . ID=Chr1:SNP:14243;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14244 14244 31.5 . . ID=Chr1:SNP:14244;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14245 14245 31.5 . . ID=Chr1:SNP:14245;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14246 14246 31.5 . . ID=Chr1:SNP:14246;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14247 14247 26 . . ID=Chr1:SNP:14247;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14248 14248 31.5 . . ID=Chr1:SNP:14248;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14249 14249 31.5 . . ID=Chr1:SNP:14249;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14250 14250 31.5 . . ID=Chr1:SNP:14250;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14251 14251 31.5 . . ID=Chr1:SNP:14251;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14252 14252 31.5 . . ID=Chr1:SNP:14252;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14253 14253 31.5 . . ID=Chr1:SNP:14253;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14254 14254 31.5 . . ID=Chr1:SNP:14254;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14255 14255 31.5 . . ID=Chr1:SNP:14255;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14256 14256 26 . . ID=Chr1:SNP:14256;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14257 14257 31.5 . . ID=Chr1:SNP:14257;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14258 14258 31.5 . . ID=Chr1:SNP:14258;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14259 14259 31.5 . . ID=Chr1:SNP:14259;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14260 14260 31.5 . . ID=Chr1:SNP:14260;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14261 14261 31.5 . . ID=Chr1:SNP:14261;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14262 14262 26 . . ID=Chr1:SNP:14262;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14263 14263 26 . . ID=Chr1:SNP:14263;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14264 14264 31.5 . . ID=Chr1:SNP:14264;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14265 14265 31.5 . . ID=Chr1:SNP:14265;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14266 14266 31.5 . . ID=Chr1:SNP:14266;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14267 14267 31.5 . . ID=Chr1:SNP:14267;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14268 14268 31.5 . . ID=Chr1:SNP:14268;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14269 14269 31.5 . . ID=Chr1:SNP:14269;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14270 14270 31.5 . . ID=Chr1:SNP:14270;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14271 14271 31.5 . . ID=Chr1:SNP:14271;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14272 14272 31.5 . . ID=Chr1:SNP:14272;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14273 14273 31.5 . . ID=Chr1:SNP:14273;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14274 14274 31.5 . . ID=Chr1:SNP:14274;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14275 14275 31.5 . . ID=Chr1:SNP:14275;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14276 14276 31.5 . . ID=Chr1:SNP:14276;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14277 14277 31.5 . . ID=Chr1:SNP:14277;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14278 14278 31.5 . . ID=Chr1:SNP:14278;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14279 14279 31.5 . . ID=Chr1:SNP:14279;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14280 14280 31.5 . . ID=Chr1:SNP:14280;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14281 14281 31.5 . . ID=Chr1:SNP:14281;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14282 14282 31.5 . . ID=Chr1:SNP:14282;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14283 14283 31.5 . . ID=Chr1:SNP:14283;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14284 14284 31.5 . . ID=Chr1:SNP:14284;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14285 14285 31.5 . . ID=Chr1:SNP:14285;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14286 14286 31.5 . . ID=Chr1:SNP:14286;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14287 14287 31.5 . . ID=Chr1:SNP:14287;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14288 14288 31.5 . . ID=Chr1:SNP:14288;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14289 14289 31.5 . . ID=Chr1:SNP:14289;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14290 14290 31.5 . . ID=Chr1:SNP:14290;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14291 14291 31.5 . . ID=Chr1:SNP:14291;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14292 14292 26 . . ID=Chr1:SNP:14292;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14293 14293 31.5 . . ID=Chr1:SNP:14293;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14294 14294 31.5 . . ID=Chr1:SNP:14294;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14295 14295 26 . . ID=Chr1:SNP:14295;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14296 14296 31.5 . . ID=Chr1:SNP:14296;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14297 14297 31.5 . . ID=Chr1:SNP:14297;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14298 14298 31.5 . . ID=Chr1:SNP:14298;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14299 14299 31.5 . . ID=Chr1:SNP:14299;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14300 14300 31.5 . . ID=Chr1:SNP:14300;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14301 14301 31.5 . . ID=Chr1:SNP:14301;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14302 14302 31.5 . . ID=Chr1:SNP:14302;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14303 14303 31.5 . . ID=Chr1:SNP:14303;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14304 14304 31.5 . . ID=Chr1:SNP:14304;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14305 14305 31.5 . . ID=Chr1:SNP:14305;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14306 14306 26 . . ID=Chr1:SNP:14306;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14307 14307 26 . . ID=Chr1:SNP:14307;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14308 14308 31.5 . . ID=Chr1:SNP:14308;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14309 14309 31.5 . . ID=Chr1:SNP:14309;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14310 14310 31.5 . . ID=Chr1:SNP:14310;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14311 14311 31.5 . . ID=Chr1:SNP:14311;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14312 14312 26 . . ID=Chr1:SNP:14312;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14313 14313 26 . . ID=Chr1:SNP:14313;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14314 14314 31.5 . . ID=Chr1:SNP:14314;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14315 14315 31.5 . . ID=Chr1:SNP:14315;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14316 14316 31.5 . . ID=Chr1:SNP:14316;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14317 14317 31.5 . . ID=Chr1:SNP:14317;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14318 14318 31.5 . . ID=Chr1:SNP:14318;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14319 14319 31.5 . . ID=Chr1:SNP:14319;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14320 14320 31.5 . . ID=Chr1:SNP:14320;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS INDEL 14320 14322 33.5 . . ID=Chr1:INDEL:14320;Variant_seq=.;Reference_seq=TC;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14321 14321 31.5 . . ID=Chr1:SNP:14321;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14322 14322 26 . . ID=Chr1:SNP:14322;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14323 14323 31.5 . . ID=Chr1:SNP:14323;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14324 14324 26 . . ID=Chr1:SNP:14324;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14325 14325 31.5 . . ID=Chr1:SNP:14325;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14326 14326 31.5 . . ID=Chr1:SNP:14326;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14327 14327 26 . . ID=Chr1:SNP:14327;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 14328 14328 31.5 . . ID=Chr1:SNP:14328;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120479 120479 31.5 . . ID=Chr1:SNP:120479;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120480 120480 31.5 . . ID=Chr1:SNP:120480;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120481 120481 31.5 . . ID=Chr1:SNP:120481;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120482 120482 31.5 . . ID=Chr1:SNP:120482;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120483 120483 31.5 . . ID=Chr1:SNP:120483;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120484 120484 31.5 . . ID=Chr1:SNP:120484;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120485 120485 31.5 . . ID=Chr1:SNP:120485;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120486 120486 31.5 . . ID=Chr1:SNP:120486;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120487 120487 31.5 . . ID=Chr1:SNP:120487;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120488 120488 31.5 . . ID=Chr1:SNP:120488;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120489 120489 31.5 . . ID=Chr1:SNP:120489;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120490 120490 31.5 . . ID=Chr1:SNP:120490;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120491 120491 31.5 . . ID=Chr1:SNP:120491;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120492 120492 31.5 . . ID=Chr1:SNP:120492;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120493 120493 31.5 . . ID=Chr1:SNP:120493;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120494 120494 31.5 . . ID=Chr1:SNP:120494;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120495 120495 31.5 . . ID=Chr1:SNP:120495;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120496 120496 31.5 . . ID=Chr1:SNP:120496;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120497 120497 31.5 . . ID=Chr1:SNP:120497;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120498 120498 26 . . ID=Chr1:SNP:120498;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120499 120499 31.5 . . ID=Chr1:SNP:120499;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120500 120500 31.5 . . ID=Chr1:SNP:120500;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120501 120501 31.5 . . ID=Chr1:SNP:120501;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120502 120502 31.5 . . ID=Chr1:SNP:120502;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120503 120503 31.5 . . ID=Chr1:SNP:120503;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120504 120504 31.5 . . ID=Chr1:SNP:120504;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120505 120505 31.5 . . ID=Chr1:SNP:120505;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120506 120506 31.5 . . ID=Chr1:SNP:120506;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120507 120507 31.5 . . ID=Chr1:SNP:120507;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120508 120508 26 . . ID=Chr1:SNP:120508;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120509 120509 31.5 . . ID=Chr1:SNP:120509;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120510 120510 31.5 . . ID=Chr1:SNP:120510;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120511 120511 31.5 . . ID=Chr1:SNP:120511;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120512 120512 31.5 . . ID=Chr1:SNP:120512;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120513 120513 31.5 . . ID=Chr1:SNP:120513;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120514 120514 31.5 . . ID=Chr1:SNP:120514;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120515 120515 26 . . ID=Chr1:SNP:120515;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120516 120516 31.5 . . ID=Chr1:SNP:120516;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120517 120517 31.5 . . ID=Chr1:SNP:120517;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120518 120518 26 . . ID=Chr1:SNP:120518;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120519 120519 31.5 . . ID=Chr1:SNP:120519;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120520 120520 31.5 . . ID=Chr1:SNP:120520;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120521 120521 31.5 . . ID=Chr1:SNP:120521;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120522 120522 31.5 . . ID=Chr1:SNP:120522;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120523 120523 31.5 . . ID=Chr1:SNP:120523;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120524 120524 31.5 . . ID=Chr1:SNP:120524;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120525 120525 31.5 . . ID=Chr1:SNP:120525;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120526 120526 31.5 . . ID=Chr1:SNP:120526;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120527 120527 31.5 . . ID=Chr1:SNP:120527;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120528 120528 31.5 . . ID=Chr1:SNP:120528;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120529 120529 31.5 . . ID=Chr1:SNP:120529;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120530 120530 31.5 . . ID=Chr1:SNP:120530;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120531 120531 31.5 . . ID=Chr1:SNP:120531;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120532 120532 31.5 . . ID=Chr1:SNP:120532;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120533 120533 31.5 . . ID=Chr1:SNP:120533;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120534 120534 31.5 . . ID=Chr1:SNP:120534;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120535 120535 31.5 . . ID=Chr1:SNP:120535;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120536 120536 31.5 . . ID=Chr1:SNP:120536;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120537 120537 31.5 . . ID=Chr1:SNP:120537;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120538 120538 31.5 . . ID=Chr1:SNP:120538;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120539 120539 31.5 . . ID=Chr1:SNP:120539;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120540 120540 31.5 . . ID=Chr1:SNP:120540;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120541 120541 31.5 . . ID=Chr1:SNP:120541;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120542 120542 31.5 . . ID=Chr1:SNP:120542;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120543 120543 31.5 . . ID=Chr1:SNP:120543;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120544 120544 31.5 . . ID=Chr1:SNP:120544;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120545 120545 31.5 . . ID=Chr1:SNP:120545;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120546 120546 31.5 . . ID=Chr1:SNP:120546;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120547 120547 31.5 . . ID=Chr1:SNP:120547;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120548 120548 31.5 . . ID=Chr1:SNP:120548;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120549 120549 31.5 . . ID=Chr1:SNP:120549;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120550 120550 31.5 . . ID=Chr1:SNP:120550;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120551 120551 31.5 . . ID=Chr1:SNP:120551;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120552 120552 31.5 . . ID=Chr1:SNP:120552;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120553 120553 26 . . ID=Chr1:SNP:120553;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120554 120554 31.5 . . ID=Chr1:SNP:120554;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120555 120555 31.5 . . ID=Chr1:SNP:120555;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120556 120556 31.5 . . ID=Chr1:SNP:120556;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120557 120557 31.5 . . ID=Chr1:SNP:120557;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120558 120558 31.5 . . ID=Chr1:SNP:120558;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120559 120559 31.5 . . ID=Chr1:SNP:120559;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120560 120560 31.5 . . ID=Chr1:SNP:120560;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120561 120561 26 . . ID=Chr1:SNP:120561;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120562 120562 31.5 . . ID=Chr1:SNP:120562;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120563 120563 31.5 . . ID=Chr1:SNP:120563;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120564 120564 31.5 . . ID=Chr1:SNP:120564;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120565 120565 31.5 . . ID=Chr1:SNP:120565;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120566 120566 31.5 . . ID=Chr1:SNP:120566;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120567 120567 31.5 . . ID=Chr1:SNP:120567;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120568 120568 31.5 . . ID=Chr1:SNP:120568;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120569 120569 31.5 . . ID=Chr1:SNP:120569;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120570 120570 31.5 . . ID=Chr1:SNP:120570;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120571 120571 26 . . ID=Chr1:SNP:120571;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120572 120572 31.5 . . ID=Chr1:SNP:120572;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120573 120573 26 . . ID=Chr1:SNP:120573;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120574 120574 31.5 . . ID=Chr1:SNP:120574;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120575 120575 26 . . ID=Chr1:SNP:120575;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120576 120576 31.5 . . ID=Chr1:SNP:120576;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120577 120577 26 . . ID=Chr1:SNP:120577;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120578 120578 26 . . ID=Chr1:SNP:120578;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120594 120594 31.5 . . ID=Chr1:SNP:120594;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120595 120595 31.5 . . ID=Chr1:SNP:120595;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120596 120596 31.5 . . ID=Chr1:SNP:120596;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120597 120597 31.5 . . ID=Chr1:SNP:120597;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120598 120598 31.5 . . ID=Chr1:SNP:120598;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120599 120599 31.5 . . ID=Chr1:SNP:120599;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120600 120600 31.5 . . ID=Chr1:SNP:120600;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120601 120601 31.5 . . ID=Chr1:SNP:120601;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120602 120602 31.5 . . ID=Chr1:SNP:120602;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120603 120603 31.5 . . ID=Chr1:SNP:120603;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120604 120604 31.5 . . ID=Chr1:SNP:120604;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120605 120605 31.5 . . ID=Chr1:SNP:120605;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120606 120606 31.5 . . ID=Chr1:SNP:120606;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120607 120607 26 . . ID=Chr1:SNP:120607;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120608 120608 31.5 . . ID=Chr1:SNP:120608;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120609 120609 31.5 . . ID=Chr1:SNP:120609;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120610 120610 31.5 . . ID=Chr1:SNP:120610;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120611 120611 31.5 . . ID=Chr1:SNP:120611;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120612 120612 31.5 . . ID=Chr1:SNP:120612;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120613 120613 31.5 . . ID=Chr1:SNP:120613;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120614 120614 31.5 . . ID=Chr1:SNP:120614;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120615 120615 31.5 . . ID=Chr1:SNP:120615;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120616 120616 31.5 . . ID=Chr1:SNP:120616;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120617 120617 26 . . ID=Chr1:SNP:120617;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120618 120618 31.5 . . ID=Chr1:SNP:120618;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120619 120619 31.5 . . ID=Chr1:SNP:120619;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120620 120620 31.5 . . ID=Chr1:SNP:120620;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120621 120621 31.5 . . ID=Chr1:SNP:120621;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120622 120622 31.5 . . ID=Chr1:SNP:120622;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120623 120623 31.5 . . ID=Chr1:SNP:120623;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120624 120624 31.5 . . ID=Chr1:SNP:120624;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120625 120625 31.5 . . ID=Chr1:SNP:120625;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120626 120626 31.5 . . ID=Chr1:SNP:120626;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120627 120627 31.5 . . ID=Chr1:SNP:120627;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120628 120628 31.5 . . ID=Chr1:SNP:120628;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120629 120629 31.5 . . ID=Chr1:SNP:120629;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120630 120630 31.5 . . ID=Chr1:SNP:120630;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120631 120631 31.5 . . ID=Chr1:SNP:120631;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120632 120632 26 . . ID=Chr1:SNP:120632;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120633 120633 31.5 . . ID=Chr1:SNP:120633;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120634 120634 26 . . ID=Chr1:SNP:120634;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120635 120635 31.5 . . ID=Chr1:SNP:120635;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120636 120636 31.5 . . ID=Chr1:SNP:120636;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120637 120637 31.5 . . ID=Chr1:SNP:120637;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120638 120638 31.5 . . ID=Chr1:SNP:120638;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120639 120639 31.5 . . ID=Chr1:SNP:120639;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120640 120640 31.5 . . ID=Chr1:SNP:120640;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120641 120641 31.5 . . ID=Chr1:SNP:120641;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120642 120642 31.5 . . ID=Chr1:SNP:120642;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120643 120643 31.5 . . ID=Chr1:SNP:120643;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120644 120644 26 . . ID=Chr1:SNP:120644;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120645 120645 31.5 . . ID=Chr1:SNP:120645;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120646 120646 26 . . ID=Chr1:SNP:120646;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120647 120647 31.5 . . ID=Chr1:SNP:120647;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120648 120648 31.5 . . ID=Chr1:SNP:120648;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120649 120649 31.5 . . ID=Chr1:SNP:120649;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120650 120650 31.5 . . ID=Chr1:SNP:120650;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120651 120651 31.5 . . ID=Chr1:SNP:120651;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120652 120652 31.5 . . ID=Chr1:SNP:120652;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120653 120653 31.5 . . ID=Chr1:SNP:120653;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120654 120654 31.5 . . ID=Chr1:SNP:120654;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120655 120655 31.5 . . ID=Chr1:SNP:120655;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120656 120656 31.5 . . ID=Chr1:SNP:120656;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120657 120657 31.5 . . ID=Chr1:SNP:120657;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120658 120658 31.5 . . ID=Chr1:SNP:120658;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120659 120659 31.5 . . ID=Chr1:SNP:120659;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120660 120660 31.5 . . ID=Chr1:SNP:120660;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120661 120661 31.5 . . ID=Chr1:SNP:120661;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120662 120662 31.5 . . ID=Chr1:SNP:120662;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120663 120663 26 . . ID=Chr1:SNP:120663;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120664 120664 26 . . ID=Chr1:SNP:120664;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120665 120665 31.5 . . ID=Chr1:SNP:120665;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120666 120666 31.5 . . ID=Chr1:SNP:120666;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120667 120667 31.5 . . ID=Chr1:SNP:120667;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120668 120668 31.5 . . ID=Chr1:SNP:120668;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120669 120669 31.5 . . ID=Chr1:SNP:120669;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120670 120670 31.5 . . ID=Chr1:SNP:120670;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120671 120671 31.5 . . ID=Chr1:SNP:120671;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120672 120672 31.5 . . ID=Chr1:SNP:120672;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120673 120673 31.5 . . ID=Chr1:SNP:120673;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120674 120674 31.5 . . ID=Chr1:SNP:120674;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120675 120675 26 . . ID=Chr1:SNP:120675;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120676 120676 26 . . ID=Chr1:SNP:120676;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120677 120677 31.5 . . ID=Chr1:SNP:120677;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120678 120678 31.5 . . ID=Chr1:SNP:120678;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120679 120679 31.5 . . ID=Chr1:SNP:120679;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120680 120680 31.5 . . ID=Chr1:SNP:120680;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120681 120681 31.5 . . ID=Chr1:SNP:120681;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120682 120682 26 . . ID=Chr1:SNP:120682;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120683 120683 26 . . ID=Chr1:SNP:120683;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120684 120684 31.5 . . ID=Chr1:SNP:120684;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120685 120685 26 . . ID=Chr1:SNP:120685;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120686 120686 26 . . ID=Chr1:SNP:120686;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120687 120687 31.5 . . ID=Chr1:SNP:120687;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120688 120688 26 . . ID=Chr1:SNP:120688;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120689 120689 31.5 . . ID=Chr1:SNP:120689;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120690 120690 26 . . ID=Chr1:SNP:120690;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120691 120691 31.5 . . ID=Chr1:SNP:120691;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120692 120692 26 . . ID=Chr1:SNP:120692;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 120693 120693 31.5 . . ID=Chr1:SNP:120693;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 1072445 1072445 26 . . ID=Chr1:SNP:1072445;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 1072446 1072446 31.5 . . ID=Chr1:SNP:1072446;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 1072447 1072447 31.5 . . ID=Chr1:SNP:1072447;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 1072448 1072448 31.5 . . ID=Chr1:SNP:1072448;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 1072449 1072449 26 . . ID=Chr1:SNP:1072449;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 1072450 1072450 31.5 . . ID=Chr1:SNP:1072450;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 1072451 1072451 26 . . ID=Chr1:SNP:1072451;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 1072452 1072452 31.5 . . ID=Chr1:SNP:1072452;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 1072453 1072453 26 . . ID=Chr1:SNP:1072453;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 1072454 1072454 26 . . ID=Chr1:SNP:1072454;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 1072455 1072455 26 . . ID=Chr1:SNP:1072455;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 1072456 1072456 31.5 . . ID=Chr1:SNP:1072456;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 1072457 1072457 31.5 . . ID=Chr1:SNP:1072457;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 1072458 1072458 31.5 . . ID=Chr1:SNP:1072458;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 1072459 1072459 26 . . ID=Chr1:SNP:1072459;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 1072460 1072460 31.5 . . ID=Chr1:SNP:1072460;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 1072461 1072461 31.5 . . ID=Chr1:SNP:1072461;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS INDEL 1072461 1072462 33.5 . . ID=Chr1:INDEL:1072461;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 1072462 1072462 31.5 . . ID=Chr1:SNP:1072462;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 1072463 1072463 31.5 . . ID=Chr1:SNP:1072463;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 1072464 1072464 31.5 . . ID=Chr1:SNP:1072464;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 1072465 1072465 31.5 . . ID=Chr1:SNP:1072465;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 1072466 1072466 31.5 . . ID=Chr1:SNP:1072466;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 1072467 1072467 32 . . ID=Chr1:SNP:1072467;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 1072468 1072468 32.4 . . ID=Chr1:SNP:1072468;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 1072469 1072469 32.4 . . ID=Chr1:SNP:1072469;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 1072470 1072470 32.4 . . ID=Chr1:SNP:1072470;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 1072471 1072471 32.4 . . ID=Chr1:SNP:1072471;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 1072472 1072472 32.4 . . ID=Chr1:SNP:1072472;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 1072473 1072473 32.4 . . ID=Chr1:SNP:1072473;Variant_seq=.;Reference_seq=C;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 1072474 1072474 32.4 . . ID=Chr1:SNP:1072474;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 1072475 1072475 32.4 . . ID=Chr1:SNP:1072475;Variant_seq=.;Reference_seq=G;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 1072476 1072476 32.4 . . ID=Chr1:SNP:1072476;Variant_seq=.;Reference_seq=T;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 1072477 1072477 32.4 . . ID=Chr1:SNP:1072477;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA +Chr1 SAMTOOLS SNP 1072478 1072478 32.4 . . ID=Chr1:SNP:1072478;Variant_seq=.;Reference_seq=A;Total_reads=1;Zygosity=NA:NA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/targets Thu May 22 20:30:19 2014 -0400 @@ -0,0 +1,5 @@ +k69_93535:SAMTOOLS:SNP:1147 +k69_93535:SAMTOOLS:SNP:1336 +k69_98089:SAMTOOLS:SNP:30 +k69_98089:SAMTOOLS:SNP:550 +k69_98089:SAMTOOLS:SNP:625
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/targets.fasta Thu May 22 20:30:19 2014 -0400 @@ -0,0 +1,44 @@ +>k69_93535 +TCATCAAATTTATCAAATTTTCCGCAGTTTCTCGCCCTCTCCACAGCGCTTTGAAGCGCT +TTTAATGGCAGCAGATGCCGCCTCAGATCTCCCAAACCGACCCATTCCTAACACTCTCAG +AAGATCCGATTCCAATTCCGTTCTACTGAACAAATACGAGCTGGGCAAGCTCCTCGGCCA +TGGAAATTTCGCCAAGGTTTACCTCGCCCGCAACCTCGCCTCCAACGAAGAAGTCGCTAT +CAAAGTCTTCGACAAAGAGAAAATCCTCAAATCCGGCCTCGTCAACCACACCAAACGCGA +GATCTCAATCCTCCGCCGTCTTCGTCATCCGAACGTCGTCGAGCTCTTCGAGGTCATGGC +CACTAAATCGAAGATCTATTTCGTCATAGAGTACGTCCGCGGTGGTGAATTATTCGGCAA +GGTAGCCAAAGGACGTCTCAACGAAAACACCGCAAGAAAGTACTTCCAGCAATTGATTTC +CGCCGTTGATTTCTGCCACGCCAGAGGCGTTTACCACAGAGATCTGAAGCCGGAAAATTT +ATTATTAGACGATAATGGTGATTTGAAGGTGTCGGATTTCGGATTGAGCGCTGTATCGGA +CCAGATGAGGCAGGATGGGTTGTTTCACACGTTTTGTGGTACTCCAGCCTACGTTGCTCC +AGAGGTTCTCGGAAGGAAAGGGTATGATGGGGCTAAGTTTGATATTTGGTCATGTGGTGT +TATTTTGTTTTTGTTGATGGCAGGGTATTTGCCCTTTCATGATCAAAATGTGATGGCTAT +GTATAAGAAGATTTATAAAGGGGAGTTCAGGTGTCCGAGATGGTTTTCAAAGGATTTGAC +ATTGTTGCTGATGAGGCTTCTCGATACAAATCCCAAAACCCGGATCACTATTCCAGAAAT +AATGGAGAATAGATGGTTCAAGAATGGATTCGAGCCTGTGAAATATTACATTGAGAATGA +TAGGTTTCATAAGTGGTGTAGCTTAGACGAAGAGAATGCTAATGACAACGAGGAGGTAGA +ATCTGGAGATGAATCAGACTCTTCAGTTGCTTCCTGCCCTCCTACACTTAATGAAGGAAA +GAAAAAAAGGACAGGGAAGCTTCATAGGCCTTTGAGTCTGAACGCATTTGACATAATTTC +CTTTTCCAGAGGATTTGATCTTTCAGGTTTGTTTGAAGAAACGGGAGATGAAACAAGATT +TGTGTCGGGTGAAACGATACCAAACATCATATCGAAATTGGAGGAGATTGCAAAAGTGGG +TAGTTTCACGTTTAGGAAGAAGGATTGTAGGGTTAGTTTAGAAGGAACGCGAGAAGGAGT +GAAGGGCCCTCTTACGATTGGAGCTGAGATATTTGAGCTTACGCCTAGTTTGGTTGTTGT +TGAGCTTAAGAAGAAAGCAGGAGACAAAGCAGAGTACGAGGAGTTTTGTAACAAGGAGTT +GAAACCTGGGTTGCTACATCTCATGTTTCCTAATGGCGGTGTTCCTTCCAACACAACTTC +TGATACAGAGTAGGCAGTGTAGGGAATTCTCAAATGTATCTGTATTATATGGCAGCGTTT +CATGATTCTTTTTGTATTAGATTTGTCGCAAGAAATTTATGTACCTTAAGATGAAAATTC +AAGTTTCA +>k69_98089 +ACAAATCCAAACATGTTATCTTCTTCTTCTTTTCCTTCTTCAAACATCCTCCTCCTCACC +AAGTCAAAATCGCTCAACGTCAGATCATCAACACGAACTTGCGCCATGGCCACCACTGCT +TCCCCATCTCCGTACGACGTGCTAGGCCTTTCGAAAGCCGCAAACTACAGCGACATAAAA +GCAGCGTATCGGAAACTGGTGCTCTCCTGCCATCCCGATGTCTGCAAACAGCCGGATGCG +TCACCGGACGAGTTTATGAAAATACACGATGCGTATTCCACGCTTTCTGATCCGGACAAG +CGTGCCGATTACGATCGGGGAAATTCATTTGGGCGTTTGAGTTATGTGAGATCTAGATCT +GCGAATTATGGTGCTCGTCGTCGAACTTGGGAGACCGATCAGTGTTGGTAAATCTAATTT +GGGGGTTTGGAGATCTATTGATTTTGTTAGGAATGGAGAAGGTCGAGGTCAGCGGTCAGC +TACGTGGGGCTAAATATTTTGAATTGATACTGAAATTCGGGAAGACTGAAAGAACGGGAT +GATAACGGTGGTAGATCCAATTAGATTGTGGAAACTTTCATGTATGCTATCTACCTAAAA +ATAATTGTGAATTTTGTGCCTCATAAGTTTGTTTGTTTAGGCATTTTTTGACTTCTGAGA +CGTTGTATGTATATTCGGCCGTTACTACTTTATTGGCTTTAATGGTGTATACTTTGTTGT +TTGCTTGTTATCCTGTACTAAATTTCT +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/targets.gff Thu May 22 20:30:19 2014 -0400 @@ -0,0 +1,31 @@ +k69_93535 SAMTOOLS INDEL 3 7 4.44 . . ID=k69_93535:SAMTOOLS:INDEL:3;Variant_seq=ATTTCACATCCCATCATCA,ATCACATCCCATCATCA;Reference_seq=ATCA;INDEL;DP=5;VDB=0.0149;AF1=1;AC1=24;DP4=0,0,3,0;MQ=23;FQ=-33.2 +k69_93535 SAMTOOLS INDEL 5 6 4.91 . . ID=k69_93535:SAMTOOLS:INDEL:5;Variant_seq=CTCATATCCCATCATC,CCGGCC;Reference_seq=C;INDEL;DP=6;VDB=0.0137;AF1=1;AC1=24;DP4=0,0,3,1;MQ=17;FQ=-32.4 +k69_93535 SAMTOOLS SNP 1141 1142 999 . . ID=k69_93535:SAMTOOLS:SNP:1141;Variant_seq=T;Reference_seq=C;DP=2644;VDB=0.0374;AF1=0.1882;AC1=5;DP4=748,786,225,294;MQ=42;FQ=999;PV4=0.037,0,0.036,0.39 +k69_93535 SAMTOOLS SNP 1147 1148 999 . . ID=k69_93535:SAMTOOLS:SNP:1147;Variant_seq=G;Reference_seq=C;DP=2645;VDB=0.0371;AF1=0.3527;G3=0.2771,0.7229,6.934e-153;HWE=0.0248;AC1=8;DP4=733,804,447,519;MQ=42;FQ=999;PV4=0.51,0,0.027,1 +k69_93535 SAMTOOLS SNP 1336 1337 999 . . ID=k69_93535:SAMTOOLS:SNP:1336;Variant_seq=A;Reference_seq=G;DP=2211;VDB=0.0395;AF1=0.4583;G3=0.08329,0.9167,1.041e-76;HWE=0.000925;AC1=11;DP4=487,645,470,542;MQ=35;FQ=999;PV4=0.12,0,0.00016,0.36 +k69_93535 SAMTOOLS SNP 3 4 27.6 . . ID=k69_93535:SAMTOOLS:SNP:3;Variant_seq=T;Reference_seq=A;DP=5;VDB=0.0198;AF1=1;AC1=24;DP4=1,0,3,1;MQ=19;FQ=-24.6;PV4=1,1,1,1 +k69_93535 SAMTOOLS SNP 661 662 999 . . ID=k69_93535:SAMTOOLS:SNP:661;Variant_seq=G;Reference_seq=A;DP=1941;VDB=0.0388;AF1=0.4584;G3=0.08304,0.917,5.651e-77;HWE=0.000923;AC1=11;DP4=553,528,368,347;MQ=42;FQ=999;PV4=0.92,0,1,1 +k69_93535 SAMTOOLS SNP 751 752 999 . . ID=k69_93535:SAMTOOLS:SNP:751;Variant_seq=A;Reference_seq=G;DP=1870;VDB=0.0363;AF1=0.5;G3=3.472e-15,1,5e-52;HWE=4.53e-05;AC1=12;DP4=512,544,345,364;MQ=42;FQ=999;PV4=0.96,6.1e-38,0.014,1 +k69_93535 SAMTOOLS SNP 887 888 999 . . ID=k69_93535:SAMTOOLS:SNP:887;Variant_seq=G;Reference_seq=A;DP=2583;VDB=0.0394;AF1=0.4583;G3=0.08333,0.9167,8.95e-52;HWE=0.000926;AC1=11;DP4=790,493,590,361;MQ=42;FQ=999;PV4=0.83,0.069,0.41,1 +k69_98089 SAMTOOLS INDEL 2 6 999 . . ID=k69_98089:SAMTOOLS:INDEL:2;Variant_seq=CAACAAA,CAAACAAA,CAAAAACAAA;Reference_seq=CAAA;INDEL;DP=430;VDB=0.0000;AF1=1;AC1=24;DP4=0,0,182,1;MQ=39;FQ=-71.8 +k69_98089 SAMTOOLS INDEL 3 6 999 . . ID=k69_98089:SAMTOOLS:INDEL:3;Variant_seq=AAAAAACAAA,AAAA;Reference_seq=AAA;INDEL;DP=451;VDB=0.0000;AF1=1;AC1=24;DP4=0,0,214,1;MQ=39;FQ=-48 +k69_98089 SAMTOOLS INDEL 4 6 999 . . ID=k69_98089:SAMTOOLS:INDEL:4;Variant_seq=AAACACTAAAAACAAA,AAA;Reference_seq=AA;INDEL;DP=468;VDB=0.0000;AF1=1;AC1=24;DP4=0,0,219,1;MQ=39;FQ=-49.3 +k69_98089 SAMTOOLS INDEL 5 6 999 . . ID=k69_98089:SAMTOOLS:INDEL:5;Variant_seq=AACTAAAAACAAA;Reference_seq=A;INDEL;DP=534;VDB=0.0000;AF1=1;AC1=24;DP4=0,0,220,1;MQ=39;FQ=-77.6 +k69_98089 SAMTOOLS INDEL 722 723 131 . . ID=k69_98089:SAMTOOLS:INDEL:722;Variant_seq=TAAAAAA;Reference_seq=T;INDEL;DP=220;VDB=0.0006;AF1=0.3195;G3=0.299,0.701,1.118e-32;HWE=0.0406;AC1=8;DP4=4,52,0,27;MQ=38;FQ=133;PV4=0.3,1,5.4e-16,0.00096 +k69_98089 SAMTOOLS INDEL 726 727 69.7 . . ID=k69_98089:SAMTOOLS:INDEL:726;Variant_seq=TAAAAA;Reference_seq=T;INDEL;DP=152;VDB=0.0007;AF1=0.2294;AC1=5;DP4=4,30,1,6;MQ=40;FQ=70.8;PV4=1,0.025,0.0063,0.079 +k69_98089 SAMTOOLS INDEL 729 731 71.6 . . ID=k69_98089:SAMTOOLS:INDEL:729;Variant_seq=TAAAAAAA;Reference_seq=TA;INDEL;DP=104;VDB=0.0010;AF1=0.3359;AC1=8;DP4=3,15,0,4;MQ=40;FQ=73.4;PV4=1,1,1,1 +k69_98089 SAMTOOLS INDEL 741 748 48.2 . . ID=k69_98089:SAMTOOLS:INDEL:741;Variant_seq=AATTTCTATTTGTTTATTATTTCT,AATTTCTATTTGTTTATTTCT,AATTTCTATTTCT;Reference_seq=AATTTCT;INDEL;DP=18;VDB=0.0050;AF1=1;AC1=24;DP4=0,0,0,9;MQ=27;FQ=-35 +k69_98089 SAMTOOLS INDEL 742 748 5.8 . . ID=k69_98089:SAMTOOLS:INDEL:742;Variant_seq=ATTTTTCT,ATTTCTATTTTCT,ATTTCTATTTTTCT;Reference_seq=ATTTCT;INDEL;DP=17;VDB=0.0022;AF1=1;AC1=24;DP4=0,0,0,3;MQ=36;FQ=-31.8 +k69_98089 SAMTOOLS INDEL 743 748 86.5 . . ID=k69_98089:SAMTOOLS:INDEL:743;Variant_seq=TTTCTATTTGTTCT,TTTCTATTTGTTTATTATTCT,TTTCTATTTGTTTATTCT;Reference_seq=TTTCT;INDEL;DP=16;VDB=0.0021;AF1=1;AC1=24;DP4=0,0,0,8;MQ=29;FQ=-34.7 +k69_98089 SAMTOOLS SNP 2 3 999 . . ID=k69_98089:SAMTOOLS:SNP:2;Variant_seq=A;Reference_seq=C;DP=430;VDB=0.0000;AF1=0.5;G3=1.09e-24,1,5.6e-21;HWE=4.53e-05;AC1=12;DP4=207,1,212,1;MQ=40;FQ=999;PV4=1,1,0.00045,1 +k69_98089 SAMTOOLS SNP 30 31 999 . . ID=k69_98089:SAMTOOLS:SNP:30;Variant_seq=G;Reference_seq=T;DP=1858;VDB=0.0011;AF1=0.5417;G3=2.023e-19,0.9167,0.08333;HWE=0.000926;AC1=13;DP4=624,74,985,116;MQ=41;FQ=999;PV4=1,0,0.00089,1 +k69_98089 SAMTOOLS SNP 3 4 999 . . ID=k69_98089:SAMTOOLS:SNP:3;Variant_seq=C;Reference_seq=A;DP=451;VDB=0.0000;AF1=0.5;G3=3.935e-24,1,2.231e-22;HWE=4.53e-05;AC1=12;DP4=226,8,205,1;MQ=40;FQ=999;PV4=0.041,1,0.00055,1 +k69_98089 SAMTOOLS SNP 453 454 31.2 . . ID=k69_98089:SAMTOOLS:SNP:453;Variant_seq=T;Reference_seq=A;DP=3692;VDB=0.0394;AF1=0.04171;AC1=1;DP4=649,868,130,171;MQ=39;FQ=31.4;PV4=0.9,0,2.3e-293,0.00051 +k69_98089 SAMTOOLS SNP 515 516 999 . . ID=k69_98089:SAMTOOLS:SNP:515;Variant_seq=G;Reference_seq=A;DP=4455;VDB=0.0378;AF1=0.4583;G3=0.08333,0.9167,1.498e-16;HWE=0.000926;AC1=11;DP4=952,817,1390,1120;MQ=33;FQ=999;PV4=0.32,0,0,1 +k69_98089 SAMTOOLS SNP 522 523 999 . . ID=k69_98089:SAMTOOLS:SNP:522;Variant_seq=G;Reference_seq=A;DP=4698;VDB=0.0388;AF1=0.4168;G3=0.1656,0.8344,2.693e-36;HWE=0.00483;AC1=10;DP4=958,914,1327,1222;MQ=35;FQ=999;PV4=0.56,0,0,1 +k69_98089 SAMTOOLS SNP 550 551 999 . . ID=k69_98089:SAMTOOLS:SNP:550;Variant_seq=A;Reference_seq=G;DP=4866;VDB=0.0385;AF1=0.5417;G3=2.024e-12,0.9167,0.08333;HWE=0.000926;AC1=13;DP4=1034,806,1547,1233;MQ=38;FQ=999;PV4=0.72,0,1e-231,1 +k69_98089 SAMTOOLS SNP 625 626 999 . . ID=k69_98089:SAMTOOLS:SNP:625;Variant_seq=G;Reference_seq=A;DP=3557;VDB=0.0340;AF1=0.5;G3=8.721e-11,1,5.503e-15;HWE=4.53e-05;AC1=12;DP4=478,825,742,1369;MQ=41;FQ=999;PV4=0.38,0,2.7e-35,0.0059 +k69_98089 SAMTOOLS SNP 693 694 999 . . ID=k69_98089:SAMTOOLS:SNP:693;Variant_seq=A;Reference_seq=T;DP=743;VDB=0.0038;AF1=0.5;G3=1.826e-14,1,3.643e-17;HWE=4.53e-05;AC1=12;DP4=37,238,66,367;MQ=39;FQ=999;PV4=0.58,6.3e-295,5.1e-12,1 +k69_98089 SAMTOOLS SNP 717 718 999 . . ID=k69_98089:SAMTOOLS:SNP:717;Variant_seq=C;Reference_seq=T;DP=284;VDB=0.0010;AF1=0.5001;G3=2.555e-19,1,4.593e-12;HWE=4.54e-05;AC1=12;DP4=5,91,8,138;MQ=36;FQ=999;PV4=1,1.9e-90,2.7e-07,6.5e-05 +k69_98089 SAMTOOLS SNP 723 724 999 . . ID=k69_98089:SAMTOOLS:SNP:723;Variant_seq=A;Reference_seq=G;DP=193;VDB=0.0010;AF1=0.4433;G3=0.08685,0.9132,1.287e-11;HWE=0.0015;AC1=11;DP4=5,79,5,45;MQ=37;FQ=999;PV4=0.5,2.9e-13,0.00011,0.47 +k69_98089 SAMTOOLS SNP 726 727 999 . . ID=k69_98089:SAMTOOLS:SNP:726;Variant_seq=C;Reference_seq=T;DP=152;VDB=0.0008;AF1=0.4943;G3=0.0835,0.8466,0.06993;HWE=0.0149;AC1=12;DP4=4,49,5,32;MQ=36;FQ=999;PV4=0.48,5.3e-32,0.00016,0.43
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/umelt_service.py Thu May 22 20:30:19 2014 -0400 @@ -0,0 +1,44 @@ +#!/usr/bin/env python + +##interrogate umelt service at Univ of Utah +import sys +import urllib +import urllib2 +import xml.etree.ElementTree as ET +import numpy as np +import scipy as sp +from scipy import interpolate +from scipy.interpolate import interp1d + + +url='https://www.dna.utah.edu/db/services/cgi-bin/udesign.cgi' +timeout_sec=500 ## default for timeout + +# Query UW melt prediction service for a single sequence, returning default array for helicity, assuming within temperature range of 65-95 +def getmelt(input_seq): + values = {'seq' : input_seq, 'rs':0, 'dmso':0,'cation': 20 ,'mg': 2} # Note the buffer conditions + data = urllib.urlencode(values) + req = urllib2.Request(url, data) + try: + response = urllib2.urlopen(req,timeout=timeout_sec) + except urllib2.HTTPError, e: + print 'The server couldn\'t fulfill the request.' + print 'Error code: ', e.code + except urllib2.URLError, e: + print 'We failed to reach a server.' + print 'Reason: ', e.reason + else: + melt_data = response.read() + tree = ET.fromstring(melt_data) + helicity = [amp.find('helicity').text.split() for amp in tree.findall('amplicon')] + hels = np.array(helicity[0], dtype=np.float32).transpose() + return hels + +# helicity[0] used because the default retreived data is a list of 3 lists (for WT, mu and hets). The 3 lists are identical for our data (no IUPAC) so only [0] is used. + +def getTm(hel_array): + temps=np.arange(65,100.5,0.5) # Temperature range of 65-100.5. Step of 0.5 NEEDS TO BE CHECKED..REcent change? + tck = interpolate.splrep(temps,hel_array,s=0) + xnew =np.arange(65,95.5,0.05) + yder = interpolate.splev(xnew,tck,der=1) # der=1, first derivative + return xnew[yder.argmin()] # Returns the x value corresponding to the minimum (peak) y value -> Tm
--- a/uniq.xml Thu Oct 18 19:47:07 2012 -0400 +++ b/uniq.xml Thu May 22 20:30:19 2014 -0400 @@ -8,5 +8,3 @@ <outputs> <data format="txt" name="outputfile" /> </outputs> - -</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vcf2gvf.py Thu May 22 20:30:19 2014 -0400 @@ -0,0 +1,68 @@ +#!/usr/bin/env python +""" +Usage vcf2gvf.py <vcf_file input> <gff_file output> +""" +import sys,re + +##simplify the variant descriptor for GVF +def get_vartype(type_str): + type_str=type_str.upper() + for V in ['COMPLEX', 'MNP', 'DEL', 'INDEL','INS','SNP']: + if V in type_str: + return V + break + + + +in_vcf_file = open(sys.argv[1], 'r') +out_gff_file = open(sys.argv[2], 'w') +out_gff_file.write("#gff-version 3\n") ####gvf-version 1.06 + +##only deal with tidy source lines, samtools is special needs +source_pat = re.compile('##source=(\S+)', re.IGNORECASE) + + +while True: + line=in_vcf_file.readline() + if line[0]!='#': + break + elif line[2:10]=='samtools': + source_type='SAMTOOLS' + break + else: + m=source_pat.match(line) + if m: + source_type=m.group(1).upper() + break + + +##now read the data +##samtools only distinguishes SNPs and indels +##This is much complicated in highly heterozygous systems +##see http://www.sequenceontology.org/miso/current_release/term/SO:0001059 +##GVF column 3 requires a type from this ontology +###vcf type may be snp, mnp, ins, del, or complex. +##for current purposes map multiple types to most complex state +##ie SNP,SNP -> SNP; SNP,MNP-> MNP; SNP,complex +try: + for line in in_vcf_file: + if line[0] != '#': + var=line.split() ##see if var[7] has indel at start. If so add TYPE=INDEL for samtools case + info_field=var[7].split(';') + if info_field[0]=='INDEL': + info_field[0]="TYPE=INDEL" + info_dict=dict(X.split('=') for X in info_field) + ##if no TYPE key, then add TYPE=SNP for samtools case + if not info_dict.has_key('TYPE'): + info_dict['TYPE']='SNP'; + var_type=get_vartype(info_dict['TYPE']) + ID=":".join([var[0],source_type,var_type,var[1]]) + start=int(var[1]) + length=len(var[3]) ## using reference length in this case + attributes=";".join(['ID='+ID,'Reference_seq='+var[3],'Variant_seq='+var[4]]) + output_line=[var[0], source_type, var_type, str(start), str(start+length-1) ,'.','.','.',attributes,"\n"] + out_gff_file.write("\t".join([str(X) for X in output_line])) +finally: + in_vcf_file.close() + out_gff_file.close() +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vcf2gvf.sh Thu May 22 20:30:19 2014 -0400 @@ -0,0 +1,47 @@ +#!/bin/sh +##convert vcf to gvf +##NOTE This is a very simple basic parser for a complex format. +#It is intended for use with mpileup output where -g or -u flags are NOT used. + +##usage vcf2gvf.sh <vcf file> <outputfile> + +#Copyright 2012 John McCallum & Leshi Chen +#New Zealand Institute for Plant and Food Research + +#New Zealand Institute for Plant and Food Research +#This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. + + + +inputfile=$1 +outputfile=$2 + +echo "##gvf-version 1.05" > $outputfile + +awk ' +BEGIN {OFS="\t"} + +##get feature type +{if (index($8,"INDEL")== 1) {type="INDEL"} else {type="SNP"} } +##get feature length +{if (type=="SNP") + {feat_length=1} + else {feat_length=length($4)} +} +{end=($2+feat_length)} + +!/^#/ { print $1 ,"SAMTOOLS",type,$2,end,$6,".",".","ID="$1":SAMTOOLS:"type":"$2";Variant_seq="$5";Reference_seq="$4";"$8} + +END {print ""} +' "$inputfile" > "$outputfile" \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vcf2gvf.xml Thu May 22 20:30:19 2014 -0400 @@ -0,0 +1,58 @@ +<?xml version="1.0"?> +<tool id="vcf2gvf_1" name="VCF to GFF3"> + <description>convert vcf to gvf/gff3</description> + <command interpreter="bash">vcf2gvf.sh $inputFile $outputfile</command> + <inputs> + <param format="vcf" name="inputFile" type="data" label="Input vcf File" help="vcf file from mpileup" /> + </inputs> + <outputs> +<data format="gff3" name="outputfile" /> + + </outputs> +<help> +This tool provides a simple conversion from vcf to gvf. + +It is intended for use with Freebayes or with Samtools mpileup + +Be sure to read the documentation to determine if it meets your requirements. + +* vcf documentation at http://samtools.sourceforge.net/samtools.shtml#6 +* GVF/GFF3 at http://www.sequenceontology.org/resources/gvf.html +* Freebayes https://github.com/ekg/freebayes + + + +**input** + +:: + + PGSC0003DMB000000010 2042429 . C A 44.6 . DP=10;VDB=0.0118;AF1=0.8295;AC1=7;DP4=2,1,3,4;MQ=20;FQ=8.78;PV4=1,5.2e-10,1,1 GT:PL:DP:GQ 0/1:14,0,42:5:23 1/1:27,6,0:2:9 1/1:15,3,0:1:7 1/1:30,6,0:2:9 + PGSC0003DMB000000038 1756646 . G A 3.69 . DP=15;VDB=0.0166;AF1=0.495;AC1=4;DP4=3,7,2,2;MQ=20;FQ=5.6;PV4=0.58,3.8e-09,1,0.31 GT:PL:DP:GQ 0/1:20,3,0:1:6 0/1:9,0,67:7:8 0/0:0,15,82:5:17 0/1:16,3,0:1:5 + PGSC0003DMB000000064 1916664 . T C 8.12 . DP=4;VDB=0.0151;AF1=1;AC1=8;DP4=0,0,0,3;MQ=20;FQ=-29.5 GT:PL:DP:GQ 1/1:14,3,0:1:5 1/1:0,0,0:0:3 1/1:13,3,0:1:5 1/1:15,3,0:1:5 + + +**output** + + +:: + + PGSC0003DMB000000010 samtools SNP 2042429 2042430 44.6 . . ID=PGSC0003DMB000000010:SAMTOOLS:SNP:2042429;Variant_seq=A;Reference_seq=C;DP=10;VDB=0.0118;AF1=0.8295;AC1=7;DP4=2,1,3,4;MQ=20;FQ=8.78;PV4=1,5.2e-10,1,1 + PGSC0003DMB000000038 samtools SNP 1756646 1756647 3.69 . . ID=PGSC0003DMB000000038:SAMTOOLS:SNP:1756646;Variant_seq=A;Reference_seq=G;DP=15;VDB=0.0166;AF1=0.495;AC1=4;DP4=3,7,2,2;MQ=20;FQ=5.6;PV4=0.58,3.8e-09,1,0.31 + PGSC0003DMB000000064 samtools SNP 1916664 1916665 8.12 . . ID=PGSC0003DMB000000064:SAMTOOLS:SNP:1916664;Variant_seq=C;Reference_seq=T;DP=4;VDB=0.0151;AF1=1;AC1=8;DP4=0,0,0,3;MQ=20;FQ=-29.5 + + + +----------------------- + +*If you use this tool please cite:* + +A Toolkit For Bulk PCR-Based Marker Design From Next-Generation Sequence Data: +Application For Development Of A Framework Linkage Map In Bulb Onion (*Allium cepa* L.) +(2012) + +Samantha Baldwin, Roopashree Revanna, Susan Thomson, Meeghan Pither-Joyce, Kathryn Wright, +Ross Crowhurst, Mark Fiers, Leshi Chen, Richard MacKnight, John A. McCallum + + +</help> +</tool>
--- a/vcf_gff.py Thu Oct 18 19:47:07 2012 -0400 +++ b/vcf_gff.py Thu May 22 20:30:19 2014 -0400 @@ -46,6 +46,8 @@ record_type = "SNP" for entry in rec: detail = entry.split("=") + if len(detail) < 2: + continue INFO[detail[0]] = detail[1] if INFO.has_key("DP"): reads = INFO.get("DP") @@ -108,7 +110,9 @@ gen = "HET" if genotypes == "0/0": gen = "HOM_ref" - else: + try: # set gen to 'NA' if still unset + gen + except NameError: gen = "NA" geno = ("%s:%s " % (reads, gen)) genos += geno @@ -141,11 +145,11 @@ end = start gen = get_gen(info[8:], reference) out_gff_file.write( - ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\tID=%s:%s:%d;Variant" + + ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\tID=%s:%s:%s:%d;Variant" + "_seq=%s;Reference_seq=%s;Total_reads=%s;Zygosity=%s\n") % ( seqid, source,record_type, start, end, score, strand, phase,seqid, - record_type, start, variant, reference, reads, gen)) - + source, record_type, start, variant, reference, reads, gen)) + out_gff_file.close()
--- a/vcf_gff.xml Thu Oct 18 19:47:07 2012 -0400 +++ b/vcf_gff.xml Thu May 22 20:30:19 2014 -0400 @@ -8,6 +8,16 @@ <outputs> <data format="gff3" name="outputfile" /> </outputs> + <tests> + <test> + <param name="inputVcf" value="mpileup_out.vcf" ftype="vcf"/> + <output name="outputfile" file="mpileup_vcf_to_gff_output.gff"/> + </test> + <test> + <param name="inputVcf" value="freebayes_out.vcf" ftype="vcf"/> + <output name="outputfile" file="freebayes_vcf_to_gff_output.gff"/> + </test> + </tests> <help> ** Convert vcf to gff3** @@ -58,4 +68,4 @@ Ross Crowhurst, Mark Fiers, Leshi Chen, Richard MacKnight, John A. McCallum </help> -</tool> \ No newline at end of file +</tool>