Table 4.
Variants count for the whole pedigree subjects and shared variants by subjects under the same pedigree group with variants location according to AnnotSV.
| Variants Filtering | Variant Count | |||
|---|---|---|---|---|
| Deletions and duplications: duphold depth based | 4314 (4120 DEL, 194 DUP) | |||
| Breakends and inversions: NA | 6857 (6560 BND, 297 INV) | |||
| Total count | BND | DEL | DUP | INV |
| <0.01 AF 1000G ALL and <0.01 gnomAD | 5492 | 1122 | 105 | 137 |
| AnnotSV ranking > 3 | 274 | 164 | 17 | 18 |
| Total length >= 50 bp | NA | 140 | 17 | 18 |
| Shared by all samples in a group | 154 (HRLS: 66; IRLS: 39; LRLS: 49) | 133 (HRLS: 48; IRLS: 46; LRLS: 39) | 4 (HRLS: 1; IRLS: 0; LRLS: 3) | 13 (HRLS: 4; IRLS: 4; LRLS: 5) |
| Shared by all samples under a particular group | 35 (HRLS: 23; IRLS: 4; LRLS: 8) | 18 (HRLS: 7; IRLS: 4; LRLS: 7) | 2 (HRLS: 0; IRLS: 0; LRLS: 2) | 2 (HRLS: 0; IRLS: 1; LRLS: 1) |
| Variant’s location according to AnnotSV | ||||
| Variants annotation according to hit from RefSeq | BND | DEL | DUP | INV |
| Intronic | 26 | 17 | 1 | 0 |
| Exonic | 2 | 0 | 0 | 0 |
| txStart-txEnd | 0 | 0 | 0 | 2 |
| NA | 7 | 1 | 1 | 0 |
RefSeq: reference sequence database; NA: not applicable; AF: allele frequency; 1000 G: 1000 genomes project for all individuals in this release; high risk to LS group (HRLS); intermediate risk to LS (IRLS); low risk to LS (LRLS); bp: base pair; BND: breakend; DEL: deletion; DUP: duplication; INV: inversion; gnomAD: Genome Aggregation Database; txStart-txEnd: Transcript Start-Transcript End.