Line 219: |
Line 219: |
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| 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;
| + | GF=0.964912,0.0350877,0;NS=57; |
− | HWEAF=0.019571;HWEGF=0.961242,0.038376,0.000383024;
| + | HWEAF=0.019571;HWEGF=0.961242,0.038376,0.000383024; |
− | MLEAF=0.0196187;MLEGF=0.960762,0.0392374,2.11537e-15;
| + | MLEAF=0.0196187;MLEGF=0.960762,0.0392374,2.11537e-15; |
− | HWE_LLR=-0.0222464;HWE_LPVAL=-0.182794;HWE_DF=1;
| + | HWE_LLR=-0.0222464;HWE_LPVAL=-0.182794;HWE_DF=1; |
− | FIC=-0.00372601;AB=0.384578
| + | FIC=-0.00372601;AB=0.384578 |
− | GT:PL:DP:AD:GQ 0/0:0,6,145:3:2,0,1:7 0/0:0,12,192:4:4,0,0:12
| + | GT:PL:DP:AD:GQ 0/0:0,6,145:3:2,0,1:7 0/0:0,12,192:4:4,0,0:12 |
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| Here is a description of the record's fields. | | Here is a description of the record's fields. |
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− | 22 : chromosome | + | 22 : chromosome |
− | 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 ATAATT. |
− | 756 : QUAL field denoting validity of this variant, higher the better. | + | 756 : QUAL field denoting validity of this variant, higher the better. |
− | PASS : a passed variant. | + | PASS : a passed variant. |
− | INFO : fields containing information about the variant. | + | AC=2... : fields containing information about the variant. |
− | FORMAT : format field labels for the genotype columns. | + | GT:PL:DP:AD:GQ : format field labels for the genotype columns. |
− | 0/0:0,6,145:3:2,0,1:7 : genotype information. | + | 0/0:0,6,145:3:2,0,1:7 : genotype information. |
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| You can obtain the same output by using the following command | | You can obtain the same output by using the following command |