Table VI.
Filtering procedure and number of remaining variants of autistic children IV2 and IV4 for each step.
| Variant | ||
|---|---|---|
|
|
||
| Filtering procedure | IV2 | IV4 |
| Total variants | 252,419 | 176,044 |
| Excluding variants if QD<2.0 or FS >60.0 or MQ<40.0 or DP<4 | 135,315 | 121,156 |
| Excluding variants if harmfulness of variant (priority) was low | 3,237 | 2,105 |
| Retaining variants if genes involved in autism in HGMD | 145 | 84 |
| Retaining variants if harmfulness of variant was high and if quality of variant was high or medium (preliminary screening gene variants in Tables I and II) | 21 | 22 |
| Following confirmation by Sanger sequencing; retaining variants if evidence score of gene was >4 in AutismKB or at ≥3 in AutDB (candidate autism–related gene variants in Tables III and IV) | 11 | 10 |
| Retaining variants if evidence score of gene was >16 in AutismKB (highly credible autism-related gene variants in Tables III and IV) | 3 | 4 |
AutDB, Autism Database; AutismKB, Autism KnowledgeBase; DP, read depth; FS, Phredscaled P-value using Fisher's exact test to detect strand bias; MQ, Root Mean Square of the mapping quality; QD, variant confidence/quality by depth.