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##fileformat=VCFv4.1
##samtoolsVersion=0.1.18 (r982:295)
##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=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=VDB,Number=1,Type=Float,Description="Variant Distance Bias">
##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=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">
##FILTER=<ID=VcfFilter,Description="VcfFilter v0.2, Expression used: ((GEN[0].PL[0]<50) & (GEN[0].PL[2]>100) & (GEN[1].PL[0]>100) & (GEN[1].PL[2]<100))">
##source_20120428.1=vcf-annotate(r731) -a /data/sequencing/refGen/dbSNP/hg19_snp132.txt.gz -c -,CHROM,FROM,TO,ID
##SnpEffVersion="2.0.5 (build 2011-12-24), by Pablo Cingolani"
##SnpEffCmd="SnpEff eff -c /data/sequencing/tools/snpEff/snpEff_2_0_5/snpEff.config -snp -onlyCoding true -o vcf -s /data/sequencing/output/biotec4/snp/final/P45/P45.html GRCh37.64 /data/sequencing/output/biotec4/snp/P45.a.diff.vcf "
##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effefct_Impact | Functional_Class | Codon_Change | Amino_Acid_change | Gene_Name | Gene_BioType | Coding | Transcript | Exon [ | ERRORS | WARNINGS ] )' ">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT /data/sequencing/output/biotec4/mapping/L774.q1.s.bam /data/sequencing/output/biotec4/mapping/L775.q1.s.bam
chr12 32491626 rs1471909 G A 124.0 . DP=22;VDB=0.0222;AF1=0.7497;AC1=3;DP4=8,0,13,0;MQ=56;FQ=113;PV4=1,8e-08,1,1;EFF=DOWNSTREAM(MODIFIER||||BICD1|protein_coding|CODING|ENST00000552160|),INTRON(MODIFIER||||BICD1|protein_coding|CODING|ENST00000281474|),INTRON(MODIFIER||||BICD1|protein_coding|CODING|ENST00000548411|),TRANSCRIPT(MODIFIER||||BICD1|protein_coding|CODING|ENST00000395758|),TRANSCRIPT(MODIFIER||||BICD1|protein_coding|CODING|ENST00000552226|) GT:PL:DP:SP:GQ 0/1:39,0,145:12:0:47 1/1:123,27,0:9:0:29
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