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Revision as of 01:14, 17 June 2014
, 01:14, 17 June 2014→Records
22 36662041 . AATAATT A 756 PASS AC=2;AN=114;AF=0.0175439;GC=55,2,0;GN=57;
22 36662041 . AATAATT A 756 PASS AC=2;AN=114;AF=0.0175439;GC=55,2,0;GN=57;
GF=0.964912,0.0350877,0;NS=57;
HWEAF=0.019571;HWEGF=0.961242,0.038376,0.000383024;
MLEAF=0.0196187;MLEGF=0.960762,0.0392374,2.11537e-15;
HWE_LLR=-0.0222464;HWE_LPVAL=-0.182794;HWE_DF=1;
FIC=-0.00372601;AB=0.384578
GT:PL:DP:AD:GQ 0/0:0,9,158:3:3,0,0:10 0/0:0,18,281:6:6,0,0:18
Here is a description of the record's fields.
Here is a description of the record's fields.
=====INFO field=====
=====INFO field=====
The information field are as follows:
The key information fields are as follows:
AC=32 : alternate allele count
AC=2 : alternate allele count
AN=116 : total number of alleles
AN=114 : total number of alleles
AF=0.28 : allele frequency based on AC/AN
AF=0.0175439 : allele frequency based on AC/AN
GC=32,20,6 : genotype counts for 0/0, 0/1, 1/1
GC=55,2,0 : genotype counts for 0/0, 0/1, 1/1
GF=0.55,0.34,0.10 : genotype frequencies based on GC
GF=0.55,0.34,0.10 : genotype frequencies based on GC
NS=58 : no. of samples
NS=57 : no. of samples
HWEAF=0.28 : genotype likelihood based estimation of the allele frequency assuming Hardy Weinberg equilibrium
HWEAF=0.28 : genotype likelihood based estimation of the allele frequency assuming Hardy Weinberg equilibrium
HWEGF=0.52,0.40,0.08 : genotype frequency derived from HWEAF
HWEGF=0.52,0.40,0.08 : genotype frequency derived from HWEAF
HWE_LPVAL=-0.182794 : log p value of HWE test
FIC=-0.00372601;AB=0.384578
FIC=-0.07 : genotype likelihood based inbreeding coefficient
FIC=-0.07 : genotype likelihood based inbreeding coefficient
AB=0.61 : genotype likelihood based allele balance
AB=0.61 : genotype likelihood based allele balance
0/0 : homozygous reference chosen based on PL
0/0 : homozygous reference chosen based on PL
0,9,108 : PHRED scaled genotype likelihoods
0,9,158 : PHRED scaled genotype likelihoods
3 : no. of reads covering this variant
3,0,6 : allele depth
3,0,0 : allele depth
counts of reads supporting the reference allele,
counts of reads supporting the reference allele,
the alternative allele and neither alleles respectively.
the alternative allele and neither alleles respectively.
