Table 1. Variant annotations and cutoff values used for SNPs identified using the low coverage data.
Annotation | Description | Cutoff value |
---|---|---|
INFO/DP | Raw read depth | >24,304 |
INFO/MQ | Average mapping quality | <34 |
INFO/MQ0F | Fraction of MQ0 reads (smaller is better) | >0.049737 |
INFO/HOB | Bias in the number of HOMs number (smaller is better) | >0.1643732 |
INFO/SGB | Segregation based metric | >2347.043 |
INFO/SGB | Segregation based metric | <-64440.286 |
QUAL | Variant quality | <20 |