Line 180: |
Line 180: |
| 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. |
Line 197: |
Line 197: |
| 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=-0.00372601;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 |