##fileformat=VCFv4.1
##fileDate=20110728
##source=freeBayes version 0.8.7
##reference=../../scaffolds/sn15_scaffolds.fasta
##phasing=none
##commandline="freebayes --bam sn4_sn15.realigned.sorted.bam --vcf sn4_sn15.realigned.freebayes.vcf --fasta-reference ../../scaffolds/sn15_scaffolds.fasta --pvar 0.0001 --show-reference-repeats --min-alternate-count 4 --min-alternate-fraction 0.5 --ploidy 1 --indels"
##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=A,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=RA,Number=1,Type=Integer,Description="Reference allele observations">
##INFO=<ID=AA,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=1,Type=Integer,Description="Homopolymer run length: the number of consecutive nucleotides in the reference genome matching the alternate allele prior to the current position">
##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=TS,Number=0,Type=Flag,Description="site has transition SNP">
##INFO=<ID=TV,Number=0,Type=Flag,Description="site has transversion SNP">
##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=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position.">
##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=1,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments">
##INFO=<ID=technology.ILLUMINA,Number=1,Type=Float,Description="Fraction of observations supporting the alternate observed in reads from ILLUMINA">
##INFO=<ID=REPEAT,Number=1,Type=String,Description="Description of the local repeat structures flanking the current position">
##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=G,Type=String,Description="Genotype Likelihood Explicit, same as GL, but with tags to indicate the specific genotype, e.g. 0=-75.22,1=-223.42,0/0=-323.03,1/0=-99.29,1/1=-802.53">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=RA,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=AA,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	sn4_01
scaffold_1	200	.	T	C	50000	.	AA=14;AB=0;ABP=0;AC=1;AF=1;AN=1;DP=15;DPRA=0;EPP=3.63072;EPPR=0;LEN=1;MQM=37;MQMR=100;NS=1;NUMALT=1;ODDS=167.908;PAIRED=0;PAIREDR=0;RA=0;REPEAT=T:3;RPP=12.937;RPPR=5.18177;RUN=1;SAP=5.49198;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.00201247;XAS=0.00201247;XRI=0;XRM=0;XRS=0;technology.ILLUMINA=1;BVAR;TS	GT:GQ:DP:RA:QR:AA:QA:GL	1:50000:14:0:0:14:870:-78.9214,0
scaffold_1	284	.	A	G	50000	.	AA=26;AB=0;ABP=0;AC=1;AF=1;AN=1;DP=27;DPRA=0;EPP=4.34659;EPPR=0;LEN=1;MQM=37;MQMR=100;NS=1;NUMALT=1;ODDS=319.174;PAIRED=0;PAIREDR=0;RA=0;REPEAT=A:2;RPP=8.35546;RPPR=5.18177;RUN=2;SAP=11.3621;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.00929756;XAS=0.00929756;XRI=0;XRM=0;XRS=0;technology.ILLUMINA=1;BVAR;TS	GT:GQ:DP:RA:QR:AA:QA:GL	1:50000:26:0:0:26:1600:-144.615,0
scaffold_1	306	.	A	G	50000	.	AA=15;AB=0;ABP=0;AC=1;AF=1;AN=1;DP=18;DPRA=0;EPP=6.62942;EPPR=3.73412;LEN=1;MQM=37;MQMR=58;NS=1;NUMALT=1;ODDS=151.941;PAIRED=0;PAIREDR=0;RA=2;RPP=20.5268;RPPR=3.73412;RUN=1;SAP=6.62942;SRP=3.73412;TYPE=snp;XAI=0;XAM=0.0132172;XAS=0.0132172;XRI=0;XRM=0.0241546;XRS=0.0241546;technology.ILLUMINA=1;BVAR;TS	GT:GQ:DP:RA:QR:AA:QA:GL	1:50000:17:2:126:15:926:-83.9573,-11.97
scaffold_1	438	.	T	C	50000	.	AA=4;AB=0;ABP=0;AC=1;AF=1;AN=1;DP=5;DPRA=0;EPP=11.6962;EPPR=0;LEN=1;MQM=37;MQMR=100;NS=1;NUMALT=1;ODDS=38.7928;PAIRED=0;PAIREDR=0;RA=0;REPEAT=T:3;RPP=11.6962;RPPR=5.18177;RUN=1;SAP=11.6962;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.0104167;XAS=0.0104167;XRI=0;XRM=0;XRS=0;technology.ILLUMINA=1;BVAR;TS	GT:GQ:DP:RA:QR:AA:QA:GL	1:168.577:4:0:0:4:247:-22.8475,0
scaffold_1	1231	.	C	T	50000	.	AA=12;AB=0;ABP=0;AC=1;AF=1;AN=1;DP=14;DPRA=0;EPP=3.73412;EPPR=3.0103;LEN=1;MQM=36.5;MQMR=68.5;NS=1;NUMALT=1;ODDS=123.564;PAIRED=0;PAIREDR=0;RA=1;REPEAT=CG:2;RPP=3.73412;RPPR=7.35324;RUN=1;SAP=3.0103;SRP=7.35324;TYPE=snp;XAI=0.0121296;XAM=0.041051;XAS=0.0289214;XRI=0.00724638;XRM=0.0289855;XRS=0.0217391;technology.ILLUMINA=1;BVAR;CpG;TS	GT:GQ:DP:RA:QR:AA:QA:GL	1:50000:13:1:61:12:724:-65.7633,-6.1
scaffold_1	1243	.	AC	A	50000	.	AA=11;AB=0;ABP=0;AC=1;AF=1;AN=1;DP=13;DPRA=0;EPP=3.20771;EPPR=7.35324;LEN=1;MQM=36.4545;MQMR=68.5;NS=1;NUMALT=1;ODDS=379.843;PAIRED=0;PAIREDR=0;RA=1;RPP=3.20771;RPPR=3.0103;RUN=1;SAP=3.20771;SRP=7.35324;TYPE=del;XAI=0;XAM=0.0436494;XAS=0.0436494;XRI=0;XRM=0.0211268;XRS=0.0211268;technology.ILLUMINA=1;BVAR	GT:GQ:DP:RA:QR:AA:QA:GL	1:50000:12:1:64:11:1951:-177.364,-6.4
scaffold_1	1519	.	C	T	50000	.	AA=10;AB=0;ABP=0;AC=1;AF=1;AN=1;DP=11;DPRA=0;EPP=6.48466;EPPR=0;LEN=1;MQM=37;MQMR=100;NS=1;NUMALT=1;ODDS=115.049;PAIRED=0;PAIREDR=0;RA=0;REPEAT=CT:2;RPP=3.87889;RPPR=5.18177;RUN=4;SAP=3.0103;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.0180381;XAS=0.0180381;XRI=0;XRM=0;XRS=0;technology.ILLUMINA=1;BVAR;TS	GT:GQ:DP:RA:QR:AA:QA:GL	1:50000:10:0:0:10:615:-55.965,0
scaffold_1	1919	.	G	A	50000	.	AA=6;AB=0;ABP=0;AC=1;AF=1;AN=1;DP=7;DPRA=0;EPP=4.45795;EPPR=0;LEN=1;MQM=37;MQMR=100;NS=1;NUMALT=1;ODDS=62.5919;PAIRED=0;PAIREDR=0;RA=0;RPP=16.0391;RPPR=5.18177;RUN=1;SAP=4.45795;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.00717834;XAS=0.00717834;XRI=0;XRM=0;XRS=0;technology.ILLUMINA=1;BVAR;TS	GT:GQ:DP:RA:QR:AA:QA:GL	1:50000:6:0:0:6:362:-33.1833,0
scaffold_1	1988	.	C	T	50000	.	AA=10;AB=0;ABP=0;AC=1;AF=1;AN=1;DP=11;DPRA=0;EPP=6.48466;EPPR=0;LEN=1;MQM=37;MQMR=100;NS=1;NUMALT=1;ODDS=113.163;PAIRED=0;PAIREDR=0;RA=0;RPP=3.87889;RPPR=5.18177;RUN=1;SAP=3.0103;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.00279734;XAS=0.00279734;XRI=0;XRM=0;XRS=0;technology.ILLUMINA=1;BVAR;TS	GT:GQ:DP:RA:QR:AA:QA:GL	1:50000:10:0:0:10:606:-55.146,0
scaffold_1	2118	.	T	C	50000	.	AA=28;AB=0;ABP=0;AC=1;AF=1;AN=1;DP=32;DPRA=0;EPP=5.80219;EPPR=5.18177;LEN=1;MQM=37.3571;MQMR=52.75;NS=1;NUMALT=1;ODDS=289.274;PAIRED=0;PAIREDR=0;RA=3;RPP=3.32051;RPPR=5.18177;RUN=2;SAP=3.0103;SRP=5.18177;TYPE=snp;XAI=0.000503018;XAM=0.0102542;XAS=0.00975121;XRI=0;XRM=0.0210344;XRS=0.0210344;technology.ILLUMINA=1;BVAR;TS	GT:GQ:DP:RA:QR:AA:QA:GL	1:50000:31:3:189:28:1652:-149.27,-17.64
scaffold_1	2433	.	C	T	50000	.	AA=6;AB=0;ABP=0;AC=1;AF=1;AN=1;DP=7;DPRA=0;EPP=16.0391;EPPR=0;LEN=1;MQM=37;MQMR=100;NS=1;NUMALT=1;ODDS=60.6923;PAIRED=0;PAIREDR=0;RA=0;REPEAT=C:2;RPP=16.0391;RPPR=5.18177;RUN=2;SAP=16.0391;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.0293118;XAS=0.0293118;XRI=0;XRM=0;XRS=0;technology.ILLUMINA=1;BVAR;TS	GT:GQ:DP:RA:QR:AA:QA:GL	1:50000:6:0:0:6:353:-32.3583,0
scaffold_1	2447	.	G	A	50000	.	AA=7;AB=0;ABP=0;AC=1;AF=1;AN=1;DP=8;DPRA=0;EPP=3.32051;EPPR=0;LEN=1;MQM=37;MQMR=100;NS=1;NUMALT=1;ODDS=77.7616;PAIRED=0;PAIREDR=0;RA=0;RPP=3.32051;RPPR=5.18177;RUN=1;SAP=10.7656;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.0291486;XAS=0.0291486;XRI=0;XRM=0;XRS=0;technology.ILLUMINA=1;BVAR;TS	GT:GQ:DP:RA:QR:AA:QA:GL	1:50000:7:0:0:7:435:-39.7714,0
scaffold_1	2455	.	T	C	50000	.	AA=6;AB=0;ABP=0;AC=1;AF=1;AN=1;DP=8;DPRA=0;EPP=8.80089;EPPR=0;LEN=1;MQM=37;MQMR=100;NS=1;NUMALT=1;ODDS=62.6961;PAIRED=0;PAIREDR=0;RA=0;REPEAT=T:3;RPP=4.45795;RPPR=5.18177;RUN=1;SAP=8.80089;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.0287983;XAS=0.0287983;XRI=0;XRM=0;XRS=0;technology.ILLUMINA=1;BVAR;TS	GT:GQ:DP:RA:QR:AA:QA:GL	1:50000:7:0:0:6:367:-37.0286,-3.8
scaffold_1	2498	.	T	C	50000	.	AA=5;AB=0;ABP=0;AC=0;AF=0;AN=1;DP=10;DPRA=0;EPP=6.91895;EPPR=6.91895;LEN=1;MQM=37;MQMR=49.6;NS=1;NUMALT=1;ODDS=0.333875;PAIRED=0;PAIREDR=0;RA=4;RPP=6.91895;RPPR=6.91895;RUN=1;SAP=3.44459;SRP=6.91895;TYPE=snp;XAI=0;XAM=0.0283483;XAS=0.0283483;XRI=0;XRM=0.0226157;XRS=0.0226157;technology.ILLUMINA=1;BVAR;TS	GT:GQ:DP:RA:QR:AA:QA:GL	0:2.34554:9:4:250:5:315:-28.98,-23.125
scaffold_1	2517	.	G	A	2.35432e-19	.	AA=6;AB=0;ABP=0;AC=0;AF=0;AN=1;DP=12;DPRA=0;EPP=16.0391;EPPR=4.45795;LEN=1;MQM=37;MQMR=47.5;NS=1;NUMALT=1;ODDS=0.741432;PAIRED=0;PAIREDR=0;RA=5;RPP=3.0103;RPPR=8.80089;RUN=1;SAP=3.0103;SRP=4.45795;TYPE=snp;XAI=0;XAM=0.0196603;XAS=0.0196603;XRI=0;XRM=0.0354353;XRS=0.0354353;technology.ILLUMINA=1;BVAR;TS	GT:GQ:DP:RA:QR:AA:QA:GL	0:1.69213:11:5:291:6:354:-32.45,-26.772
scaffold_1	2555	.	A	G	1.24779e-17	.	AA=17;AB=0;ABP=0;AC=1;AF=1;AN=1;DP=31;DPRA=0;EPP=3.13803;EPPR=3.0103;LEN=1;MQM=37;MQMR=41.5;NS=1;NUMALT=1;ODDS=29.024;PAIRED=0;PAIREDR=0;RA=13;REPEAT=A:2;RPP=18.4661;RPPR=33.4109;RUN=2;SAP=3.13803;SRP=3.63072;TYPE=snp;XAI=0.00096432;XAM=0.019366;XAS=0.0184017;XRI=0;XRM=0.0302627;XRS=0.0302627;technology.ILLUMINA=1;BVAR;TS	GT:GQ:DP:RA:QR:AA:QA:GL	1:126.05:30:13:811:17:1018:-92.2188,-73.6138
scaffold_1	4212	.	T	C	50000	.	AA=5;AB=0;ABP=0;AC=1;AF=1;AN=1;DP=6;DPRA=0;EPP=3.44459;EPPR=0;LEN=1;MQM=37;MQMR=100;NS=1;NUMALT=1;ODDS=51.8542;PAIRED=0;PAIREDR=0;RA=0;RPP=13.8677;RPPR=5.18177;RUN=1;SAP=3.44459;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.0145509;XAS=0.0145509;XRI=0;XRM=0;XRS=0;technology.ILLUMINA=1;BVAR;CpG;TS	GT:GQ:DP:RA:QR:AA:QA:GL	1:50000:5:0:0:5:310:-28.52,0
scaffold_1	4251	.	G	A	50000	.	AA=13;AB=0;ABP=0;AC=1;AF=1;AN=1;DP=14;DPRA=0;EPP=4.51363;EPPR=0;LEN=1;MQM=37;MQMR=100;NS=1;NUMALT=1;ODDS=156.314;PAIRED=0;PAIREDR=0;RA=0;RPP=3.17734;RPPR=5.18177;RUN=1;SAP=4.51363;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.0110764;XAS=0.0110764;XRI=0;XRM=0;XRS=0;technology.ILLUMINA=1;BVAR;TS	GT:GQ:DP:RA:QR:AA:QA:GL	1:50000:13:0:0:13:814:-73.8862,0
scaffold_1	4293	.	G	C	7.06295e-19	.	AA=4;AB=0;ABP=0;AC=1;AF=1;AN=1;DP=5;DPRA=0;EPP=5.18177;EPPR=0;LEN=1;MQM=37;MQMR=100;NS=1;NUMALT=1;ODDS=37.5149;PAIRED=0;PAIREDR=0;RA=0;REPEAT=G:3;RPP=11.6962;RPPR=5.18177;RUN=1;SAP=5.18177;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.0178097;XAS=0.0178097;XRI=0;XRM=0;XRS=0;technology.ILLUMINA=1;BVAR;TV	GT:GQ:DP:RA:QR:AA:QA:GL	1:162.909:4:0:0:4:241:-22.2925,0
scaffold_1	4326	.	G	T	50000	.	AA=4;AB=0;ABP=0;AC=1;AF=1;AN=1;DP=5;DPRA=0;EPP=11.6962;EPPR=0;LEN=1;MQM=37;MQMR=100;NS=1;NUMALT=1;ODDS=37.0889;PAIRED=0;PAIREDR=0;RA=0;RPP=11.6962;RPPR=5.18177;RUN=1;SAP=11.6962;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.0105145;XAS=0.0105145;XRI=0;XRM=0;XRS=0;technology.ILLUMINA=1;BVAR;TV	GT:GQ:DP:RA:QR:AA:QA:GL	1:161.076:4:0:0:4:239:-22.1075,0
scaffold_1	4432	.	T	A	50000	.	AA=19;AB=0;ABP=0;AC=1;AF=1;AN=1;DP=20;DPRA=0;EPP=3.12459;EPPR=0;LEN=1;MQM=37;MQMR=100;NS=1;NUMALT=1;ODDS=232.774;PAIRED=0;PAIREDR=0;RA=0;REPEAT=TA:3;RPP=5.8675;RPPR=5.18177;RUN=3;SAP=3.12459;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.00149377;XAS=0.00149377;XRI=0;XRM=0;XRS=0;technology.ILLUMINA=1;BVAR;TV	GT:GQ:DP:RA:QR:AA:QA:GL	1:50000:19:0:0:19:1183:-107.093,0
scaffold_1	4886	.	G	A	50000	.	AA=14;AB=0;ABP=0;AC=1;AF=1;AN=1;DP=15;DPRA=0;EPP=5.49198;EPPR=0;LEN=1;MQM=37;MQMR=100;NS=1;NUMALT=1;ODDS=163.73;PAIRED=0;PAIREDR=0;RA=0;RPP=3.63072;RPPR=5.18177;RUN=1;SAP=3.0103;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.0111263;XAS=0.0111263;XRI=0;XRM=0;XRS=0;technology.ILLUMINA=1;BVAR;TS	GT:GQ:DP:RA:QR:AA:QA:GL	1:50000:14:0:0:14:850:-77.1071,0
scaffold_1	4904	.	T	C	50000	.	AA=16;AB=0;ABP=0;AC=1;AF=1;AN=1;DP=17;DPRA=0;EPP=3.0103;EPPR=0;LEN=1;MQM=37;MQMR=100;NS=1;NUMALT=1;ODDS=192.77;PAIRED=0;PAIREDR=0;RA=0;RPP=3.55317;RPPR=5.18177;RUN=1;SAP=3.55317;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.00792392;XAS=0.00792392;XRI=0;XRM=0;XRS=0;technology.ILLUMINA=1;BVAR;TS	GT:GQ:DP:RA:QR:AA:QA:GL	1:50000:16:0:0:16:990:-89.7188,0
scaffold_1	5058	.	G	A	50000	.	AA=11;AB=0;ABP=0;AC=1;AF=1;AN=1;DP=12;DPRA=0;EPP=4.78696;EPPR=0;LEN=1;MQM=37;MQMR=100;NS=1;NUMALT=1;ODDS=132.503;PAIRED=0;PAIREDR=0;RA=0;RPP=26.8965;RPPR=5.18177;RUN=2;SAP=4.78696;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.0115069;XAS=0.0115069;XRI=0;XRM=0;XRS=0;technology.ILLUMINA=1;BVAR;TS	GT:GQ:DP:RA:QR:AA:QA:GL	1:50000:11:0:0:11:699:-63.5455,0
scaffold_1	5079	.	G	A	2.82518e-18	.	AA=5;AB=0;ABP=0;AC=1;AF=1;AN=1;DP=7;DPRA=0;EPP=6.91895;EPPR=7.35324;LEN=1;MQM=37;MQMR=68.5;NS=1;NUMALT=1;ODDS=34.5756;PAIRED=0;PAIREDR=0;RA=1;RPP=13.8677;RPPR=7.35324;RUN=2;SAP=6.91895;SRP=3.0103;TYPE=snp;XAI=0;XAM=0.0253152;XAS=0.0253152;XRI=0.00735294;XRM=0.0294118;XRS=0.0220588;technology.ILLUMINA=1;BVAR;TS	GT:GQ:DP:RA:QR:AA:QA:GL	1:150.157:6:1:64:5:298:-27.416,-6.4
scaffold_1	5082	.	T	C	50000	.	AA=4;AB=0;ABP=0;AC=1;AF=1;AN=1;DP=6;DPRA=0;EPP=11.6962;EPPR=7.35324;LEN=1;MQM=37;MQMR=68.5;NS=1;NUMALT=1;ODDS=17.4709;PAIRED=0;PAIREDR=0;RA=1;REPEAT=T:2;RPP=11.6962;RPPR=7.35324;RUN=2;SAP=11.6962;SRP=3.0103;TYPE=snp;XAI=0;XAM=0.0281718;XAS=0.0281718;XRI=0.00735294;XRM=0.0294118;XRS=0.0220588;technology.ILLUMINA=1;BVAR;TS	GT:GQ:DP:RA:QR:AA:QA:GL	1:75.875:5:1:63:4:215:-19.8875,-6.3
scaffold_1	5114	.	C	T	6.59208e-18	.	AA=7;AB=0;ABP=0;AC=0;AF=0;AN=1;DP=15;DPRA=0;EPP=3.32051;EPPR=4.09604;LEN=1;MQM=37;MQMR=44.875;NS=1;NUMALT=1;ODDS=15.9207;PAIRED=0;PAIREDR=0;RA=7;RPP=18.2106;RPPR=20.3821;RUN=4;SAP=3.32051;SRP=3.0103;TYPE=snp;XAI=0;XAM=0.0142299;XAS=0.0142299;XRI=0.00183824;XRM=0.0391249;XRS=0.0372867;technology.ILLUMINA=1;TS	GT:GQ:DP:RA:QR:AA:QA:GL	0:69.1429:14:7:438:7:428:-39.1314,-40.0457
scaffold_1	5120	.	G	A	50000	.	AA=7;AB=0;ABP=0;AC=1;AF=1;AN=1;DP=8;DPRA=0;EPP=3.32051;EPPR=0;LEN=1;MQM=37;MQMR=100;NS=1;NUMALT=1;ODDS=78.1826;PAIRED=0;PAIREDR=0;RA=0;RPP=18.2106;RPPR=5.18177;RUN=2;SAP=3.32051;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.0142299;XAS=0.0142299;XRI=0;XRM=0;XRS=0;technology.ILLUMINA=1;BVAR;CpG;TS	GT:GQ:DP:RA:QR:AA:QA:GL	1:50000:7:0:0:7:437:-39.9543,0
scaffold_1	5149	.	T	A	50000	.	AA=10;AB=0;ABP=0;AC=0;AF=0;AN=1;DP=21;DPRA=0;EPP=3.87889;EPPR=3.20771;LEN=1;MQM=37;MQMR=42.7273;NS=1;NUMALT=1;ODDS=7.52945;PAIRED=0;PAIREDR=0;RA=10;REPEAT=T:4|TA:2;RPP=3.87889;RPPR=19.0002;RUN=2;SAP=3.87889;SRP=3.20771;TYPE=snp;XAI=0;XAM=0.0252979;XAS=0.0252979;XRI=0;XRM=0.0219713;XRS=0.0219713;technology.ILLUMINA=1;BVAR;TV	GT:GQ:DP:RA:QR:AA:QA:GL	0:0.00233167:20:10:608:10:638:-58.058,-55.328
scaffold_1	5188	.	T	C	50000	.	AA=13;AB=0;ABP=0;AC=0;AF=0;AN=1;DP=26;DPRA=0;EPP=3.17734;EPPR=3.17734;LEN=1;MQM=37;MQMR=41.8462;NS=1;NUMALT=1;ODDS=5.35823;PAIRED=0;PAIREDR=0;RA=12;REPEAT=T:3;RPP=7.18621;RPPR=7.18621;RUN=1;SAP=3.17734;SRP=11.1951;TYPE=snp;XAI=0;XAM=0.00323694;XAS=0.00323694;XRI=0;XRM=0.0347944;XRS=0.0347944;technology.ILLUMINA=1;BVAR;TS	GT:GQ:DP:RA:QR:AA:QA:GL	0:0.0204039:25:12:758:13:799:-72.5246,-68.8517
scaffold_1	5198	.	C	T	1.76574e-17	.	AA=13;AB=0;ABP=0;AC=1;AF=1;AN=1;DP=25;DPRA=0;EPP=3.17734;EPPR=3.73412;LEN=1;MQM=37;MQMR=42.25;NS=1;NUMALT=1;ODDS=13.3508;PAIRED=0;PAIREDR=0;RA=11;REPEAT=C:2;RPP=11.1951;RPPR=21.1059;RUN=2;SAP=11.1951;SRP=3.73412;TYPE=snp;XAI=0;XAM=0.0228405;XAS=0.0228405;XRI=0;XRM=0.0163733;XRS=0.0163733;technology.ILLUMINA=1;BVAR;TS	GT:GQ:DP:RA:QR:AA:QA:GL	1:57.9818:24:11:662:13:793:-71.98,-60.1818
scaffold_1	5228	.	G	A	50000	.	AA=20;AB=0;ABP=0;AC=0;AF=0;AN=1;DP=40;DPRA=0;EPP=4.74748;EPPR=3.44459;LEN=1;MQM=37;MQMR=40.15;NS=1;NUMALT=1;ODDS=3.0502;PAIRED=0;PAIREDR=0;RA=19;RPP=4.74748;RPPR=3.0103;RUN=1;SAP=9.95901;SRP=3.0103;TYPE=snp;XAI=0;XAM=0.0121131;XAS=0.0121131;XRI=0;XRM=0.00768025;XRS=0.00768025;technology.ILLUMINA=1;BVAR;TS	GT:GQ:DP:RA:QR:AA:QA:GL	0:0.200916:39:19:1166:20:1218:-110.229,-105.554
scaffold_1	5449	.	C	T	50000	.	AA=46;AB=0;ABP=0;AC=1;AF=1;AN=1;DP=47;DPRA=0;EPP=12.2627;EPPR=0;LEN=1;MQM=37;MQMR=100;NS=1;NUMALT=1;ODDS=580.925;PAIRED=0;PAIREDR=0;RA=0;REPEAT=C:2;RPP=7.73089;RPPR=5.18177;RUN=1;SAP=3.19912;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.0181378;XAS=0.0181378;XRI=0;XRM=0;XRS=0;technology.ILLUMINA=1;BVAR;TS	GT:GQ:DP:RA:QR:AA:QA:GL	1:50000:46:0:0:46:2863:-258.292,0
scaffold_1	5464	.	T	C	50000	.	AA=29;AB=0;ABP=0;AC=1;AF=1;AN=1;DP=40;DPRA=0;EPP=3.68421;EPPR=0;LEN=1;MQM=37;MQMR=100;NS=1;NUMALT=1;ODDS=346.106;PAIRED=0;PAIREDR=0;RA=0;REPEAT=TCTAT:2;RPP=24.6501;RPPR=5.18177;RUN=2;SAP=3.08518;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.0186153;XAS=0.0186153;XRI=0;XRM=0;XRS=0;technology.ILLUMINA=1;BVAR;TS	GT:GQ:DP:RA:QR:AA:QA:GL	1:50000:39:0:0:29:1737:-213.005,-56.693
scaffold_1	5510	.	C	T	50000	.	AA=20;AB=0;ABP=0;AC=1;AF=1;AN=1;DP=21;DPRA=0;EPP=4.74748;EPPR=0;LEN=1;MQM=37;MQMR=100;NS=1;NUMALT=1;ODDS=242.288;PAIRED=0;PAIREDR=0;RA=0;RPP=3.0103;RPPR=5.18177;RUN=5;SAP=4.74748;SRP=5.18177;TYPE=snp;XAI=0.000714286;XAM=0.0106204;XAS=0.00990609;XRI=0;XRM=0;XRS=0;technology.ILLUMINA=1;BVAR;TS	GT:GQ:DP:RA:QR:AA:QA:GL	1:50000:20:0:0:20:1229:-111.225,0
scaffold_1	5627	.	G	C	50000	.	AA=24;AB=0;ABP=0;AC=1;AF=1;AN=1;DP=40;DPRA=0;EPP=8.80089;EPPR=3.55317;LEN=1;MQM=37;MQMR=40.9375;NS=1;NUMALT=1;ODDS=97.8721;PAIRED=0;PAIREDR=0;RA=15;RPP=20.744;RPPR=7.89611;RUN=1;SAP=3.37221;SRP=3.55317;TYPE=snp;XAI=0;XAM=0.0178408;XAS=0.0178408;XRI=0;XRM=0.00635584;XRS=0.00635584;technology.ILLUMINA=1;BVAR;TV	GT:GQ:DP:RA:QR:AA:QA:GL	1:50000:39:15:917:24:1456:-131.647,-83.1413
scaffold_1	5641	.	C	T	50000	.	AA=19;AB=0;ABP=0;AC=1;AF=1;AN=1;DP=31;DPRA=0;EPP=3.12459;EPPR=3.73412;LEN=1;MQM=37;MQMR=42.25;NS=1;NUMALT=1;ODDS=93.5682;PAIRED=0;PAIREDR=0;RA=11;REPEAT=CT:2;RPP=4.03889;RPPR=29.068;RUN=2;SAP=5.8675;SRP=3.0103;TYPE=snp;XAI=0;XAM=0.0233765;XAS=0.0233765;XRI=0;XRM=0.0108756;XRS=0.0108756;technology.ILLUMINA=1;BVAR;TS	GT:GQ:DP:RA:QR:AA:QA:GL	1:50000:30:11:670:19:1188:-107.545,-60.9091
scaffold_1	5671	.	C	G	50000	.	AA=43;AB=0;ABP=0;AC=1;AF=1;AN=1;DP=44;DPRA=0;EPP=3.0608;EPPR=0;LEN=1;MQM=37;MQMR=100;NS=1;NUMALT=1;ODDS=530.745;PAIRED=0;PAIREDR=0;RA=0;RPP=17.6046;RPPR=5.18177;RUN=1;SAP=3.46479;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.00874525;XAS=0.00874525;XRI=0;XRM=0;XRS=0;technology.ILLUMINA=1;BVAR;TV	GT:GQ:DP:RA:QR:AA:QA:GL	1:50000:43:0:0:43:2621:-236.5,0
scaffold_1	5766	.	T	C	50000	.	AA=36;AB=0;ABP=0;AC=1;AF=1;AN=1;DP=55;DPRA=0;EPP=5.18177;EPPR=3.12459;LEN=1;MQM=37;MQMR=40.3158;NS=1;NUMALT=1;ODDS=211.233;PAIRED=0;PAIREDR=0;RA=18;REPEAT=TA:3;RPP=11.6962;RPPR=3.12459;RUN=1;SAP=3.25157;SRP=12.2676;TYPE=snp;XAI=0;XAM=0.0202881;XAS=0.0202881;XRI=0;XRM=0.00147228;XRS=0.00147228;technology.ILLUMINA=1;BVAR;TS	GT:GQ:DP:RA:QR:AA:QA:GL	1:50000:54:18:1096:36:2182:-196.986,-99.2489
scaffold_1	5772	.	A	G	50000	.	AA=30;AB=0;ABP=0;AC=1;AF=1;AN=1;DP=49;DPRA=0;EPP=3.29983;EPPR=3.12459;LEN=1;MQM=37;MQMR=40.3158;NS=1;NUMALT=1;ODDS=144.739;PAIRED=0;PAIREDR=0;RA=18;REPEAT=A:6;RPP=17.1973;RPPR=4.03889;RUN=1;SAP=3.29983;SRP=5.8675;TYPE=snp;XAI=0;XAM=0.02246;XAS=0.02246;XRI=0;XRM=0.00294457;XRS=0.00294457;technology.ILLUMINA=1;BVAR;TS	GT:GQ:DP:RA:QR:AA:QA:GL	1:50000:48:18:1105:30:1870:-168.923,-100.064
scaffold_1	5830	.	A	T	50000	.	AA=17;AB=0;ABP=0;AC=1;AF=1;AN=1;DP=19;DPRA=0;EPP=4.1599;EPPR=7.35324;LEN=1;MQM=37;MQMR=68.5;NS=1;NUMALT=1;ODDS=185.187;PAIRED=0;PAIREDR=0;RA=1;RPP=4.1599;RPPR=7.35324;RUN=4;SAP=6.20364;SRP=3.0103;TYPE=snp;XAI=0;XAM=0.0158101;XAS=0.0158101;XRI=0;XRM=0;XRS=0;technology.ILLUMINA=1;BVAR;TV	GT:GQ:DP:RA:QR:AA:QA:GL	1:50000:18:1:38:17:996:-90.2259,-3.8
scaffold_1	5844	.	A	G	50000	.	AA=14;AB=0;ABP=0;AC=1;AF=1;AN=1;DP=16;DPRA=0;EPP=8.59409;EPPR=0;LEN=1;MQM=37;MQMR=100;NS=1;NUMALT=1;ODDS=162.633;PAIRED=0;PAIREDR=0;RA=0;RPP=25.3454;RPPR=5.18177;RUN=1;SAP=5.49198;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.0181319;XAS=0.0181319;XRI=0;XRM=0;XRS=0;technology.ILLUMINA=1;BVAR;CpG;TS	GT:GQ:DP:RA:QR:AA:QA:GL	1:50000:15:0:0:14:849:-80.3307,-3.7
scaffold_1	5869	.	C	G	50000	.	AA=21;AB=0;ABP=0;AC=1;AF=1;AN=1;DP=22;DPRA=0;EPP=8.07707;EPPR=0;LEN=1;MQM=37;MQMR=100;NS=1;NUMALT=1;ODDS=250.971;PAIRED=0;PAIREDR=0;RA=0;RPP=20.4855;RPPR=5.18177;RUN=3;SAP=8.07707;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.0168737;XAS=0.0168737;XRI=0;XRM=0;XRS=0;technology.ILLUMINA=1;BVAR;TV	GT:GQ:DP:RA:QR:AA:QA:GL	1:50000:21:0:0:21:1271:-114.995,0
scaffold_1	5884	.	A	G	50000	.	AA=27;AB=0;ABP=0;AC=1;AF=1;AN=1;DP=28;DPRA=0;EPP=16.6021;EPPR=0;LEN=1;MQM=37;MQMR=100;NS=1;NUMALT=1;ODDS=327.028;PAIRED=0;PAIREDR=0;RA=0;REPEAT=A:2|AAGC:2;RPP=61.6401;RPPR=5.18177;RUN=1;SAP=16.6021;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.0132516;XAS=0.0132516;XRI=0;XRM=0;XRS=0;technology.ILLUMINA=1;BVAR;CpG;TS	GT:GQ:DP:RA:QR:AA:QA:GL	1:50000:27:0:0:27:1638:-148.027,0
scaffold_1	5967	.	T	A	50000	.	AA=19;AB=0;ABP=0;AC=1;AF=1;AN=1;DP=20;DPRA=0;EPP=4.03889;EPPR=0;LEN=1;MQM=37;MQMR=100;NS=1;NUMALT=1;ODDS=229.022;PAIRED=0;PAIREDR=0;RA=0;REPEAT=T:2;RPP=4.03889;RPPR=5.18177;RUN=2;SAP=3.12459;SRP=5.18177;TYPE=snp;XAI=0;XAM=0.00917277;XAS=0.00917277;XRI=0;XRM=0;XRS=0;technology.ILLUMINA=1;BVAR;TV	GT:GQ:DP:RA:QR:AA:QA:GL	1:50000:19:0:0:19:1165:-105.463,0
scaffold_1	5984	.	T	C	50000	.	AA=16;AB=0;ABP=0;AC=1;AF=1;AN=1;DP=18;DPRA=0;EPP=3.55317;EPPR=3.0103;LEN=1;MQM=37;MQMR=68.5;NS=1;NUMALT=1;ODDS=175.032;PAIRED=0;PAIREDR=0;RA=1;REPEAT=T:2;RPP=3.55317;RPPR=7.35324;RUN=1;SAP=5.18177;SRP=7.35324;TYPE=snp;XAI=0;XAM=0.0108927;XAS=0.0108927;XRI=0;XRM=0.0220588;XRS=0.0220588;technology.ILLUMINA=1;BVAR;TS	GT:GQ:DP:RA:QR:AA:QA:GL	1:50000:17:1:58:16:969:-87.8156,-5.8
scaffold_1	6135	.	T	C	50000	.	AA=14;AB=0;ABP=0;AC=1;AF=1;AN=1;DP=15;DPRA=0;EPP=3.63072;EPPR=0;LEN=1;MQM=37;MQMR=100;NS=1;NUMALT=1;ODDS=163.104;PAIRED=0;PAIREDR=0;RA=0;REPEAT=T:6;RPP=3.63072;RPPR=5.18177;RUN=1;SAP=8.59409;SRP=5.18177;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;technology.ILLUMINA=1;BVAR;TS	GT:GQ:DP:RA:QR:AA:QA:GL	1:50000:14:0:0:14:847:-76.835,0
scaffold_1	6341	.	T	C	50000	.	AA=18;AB=0;ABP=0;AC=1;AF=1;AN=1;DP=19;DPRA=0;EPP=3.0103;EPPR=0;LEN=1;MQM=37;MQMR=100;NS=1;NUMALT=1;ODDS=215.548;PAIRED=0;PAIREDR=0;RA=0;REPEAT=T:2;RPP=4.9405;RPPR=5.18177;RUN=1;SAP=3.49285;SRP=5.18177;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;technology.ILLUMINA=1;BVAR;TS	GT:GQ:DP:RA:QR:AA:QA:GL	1:50000:18:0:0:18:1100:-99.6111,0