1,102
edits
Changes
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Revision as of 03:32, 17 June 2014
, 03:32, 17 June 2014→Records
36662041 : genome position
36662041 : genome position
. : this is the ID field that is left blank.
. : this is the ID field that is left blank.
AATAATT : the reference sequence that is replaced by the alternative sequence below.
AATAATT : the reference sequence that is replaced by the alternative sequence below.
A : so this is basically a deletion of GT
A : so this is basically a deletion of GT
756 : QUAL field denoting validity of this variant, higher the better.
756 : QUAL field denoting validity of this variant, higher the better.
The key information fields are as follows:
The key information fields are as follows:
AC=2 : alternate allele count
AC=2 : alternate allele count
AN=114 : total number of alleles
AN=114 : total number of alleles
AF=0.0175439 : allele frequency based on AC/AN
AF=0.017 : allele frequency based on AC/AN
GC=55,2,0 : 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=57 : 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
HWE_LPVAL=-1.08 : log p value of HWE test
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
