Table 3. Variant annotations and cutoff values used for SNPs identified using the exome data.
Annotation | Description | Cutoff value |
---|---|---|
INFO/DP | Raw read depth | >656,519 |
INFO/MQ | Average mapping quality | <38 |
INFO/MQ0F | Fraction of MQ0 reads (smaller is better) | >0.0146629 |
INFO/HOB | Bias in the number of HOMs number (smaller is better) | >0.1536016 |
INFO/SGB | Segregation based metric | >57489.21 |
INFO/SGB | Segregation based metric | <-226326.93 |
QUAL | Variant quality | <20 |