Table 1 Alignment features used for machine learning
Feature type | Extraction | Technical notes |
|---|---|---|
(A) Per read alignment | ||
AS: Alignment Score ED: Edit Distance MM: Mismatch count HQMM: HQ mismatch count GO: Gap Open count GE: Gap Extend count INS: Insertion count HQINS: HQ insertion count DELS: Deletion count HQDEL: HQ deletion count | Taken from: ● P1 R1, ● P1 R2, ● P2 R1, ● P2 R2 10 feature types, 40 features total | High-quality (HQ) means that the base call quality score is the maximal value. The HQ requirement was applied to the one base involved in a mismatch or insertion, and to the two surrounding bases for deletion. INS or DEL refer to an extra or missing base in the read, respectively. GO is the number of separate indels, and GE is the number of bases in indels |
(B) Compare totals per parent | ||
AS diff ED diff MM diff HQMM diff GO diff GE diff INS diff DELS diff HQINS diff HQDEL diff MAT diff | Subtract (P1 R1 + P1 R2) from (P2 R1 + P2 R2) | Each difference represents the sum over the read pair alignments to parent 2 minus the equivalent sum for parent 1 MAT is the matched base count. See A) for other feature types |
(C) Compare spans per parent | ||
Span diff | Subtract P1 span from P2 span | Span is the length of the read pair alignment along the reference |
(D) The better alignment score | ||
Parent choice | Compare P1 to P2 | Use -1 or + 1 to indicate whether P1 or P2 had the greater alignment score, respectively, or 0 if tied |