Table 1.
Summary of variant types and discovery methods. SNVs and indels were detected using the Genome Analysis Toolkit (GATK) and SVs were detected by breakpoint evidence (BP) and supported by read-depth evidence (BP, RD), or only detected by read-depth evidence (RD). Common variants (MAF ≥ 0.05) were tested for cis eQTLs. The SV-only eQTL mapping excluded SNVs and indels for greater sensitivity, while the joint eQTL mapping included all variant types.
| Detection method | # of variants | Median resolution (bp) | Median size (bp) | # of common variants | eVariants (SV-only) | eVariants (joint) | |
|---|---|---|---|---|---|---|---|
| SNV | GATK | 21,764,904 | – | 1 | 6,394,161 | – | 16,959 |
| Indel | GATK | 3,030,964 | – | 3 | 801,431 | – | 2,130 |
| Deletion (DEL) | BP, RD | 11,492 | 35 | 993 | 2,939 | 510 | 25 |
| RD | 473 | kilobase* | 3,819 | 284 | 68 | 17 | |
| Duplication (DUP) | BP, RD | 2,506 | 96 | 576 | 676 | 97 | 3 |
| RD | 1,035 | kilobase* | 4,999 | 684 | 148 | 76 | |
| Multi-allelic CNV (mCNV) | RD | 1,534 | kilobase* | 3,847 | 1060 | 264 | 118 |
| Inversion (INV) | BP | 51 | 15 | 1045 | 14 | 0 | 0 |
| Reference mobile element insertion (rMEI) | BP | 2,051 | 1 | 307 | 1,535 | 265 | 10 |
| Other SV (BND) | BP | 4,460 | 34 | – | 1,788 | 281 | 4 |
| All SVs | – | 23,602 | 39 | – | 8,980 | 1,634 | 253 |
| All variant types | – | 24,819,470 | – | – | 7,204,572 | – | 19,342 |
*
Resolution refers to the positional certainty at each breakpoint, with read-depth variants having approximate breakpoint precision on the kilobase scale.