Table 4.
VEP-reported effects of algorithm-specific variants in essential genes of Altai Neandertal
| Algorithm-specific calls |
|||
|---|---|---|---|
| ARIADNA | snpAD | GATK | |
| Stop lost | 0 | 0 | 3 |
| Missense variant | 0 | 0 | 101 |
| Stop gained | 0 | 0 | 8 |
| Upstream gene variant | 2 | 7 | 1,056 |
| Non-coding transcript variant | 2 | 11 | 1,091 |
| Splice acceptor variant | 0 | 0 | 3 |
| 3 prime UTR variant | 0 | 0 | 171 |
| Incomplete terminal codon variant | 0 | 0 | 1 |
| Synonymous variant | 0 | 0 | 48 |
| Non-coding transcript exon variant | 1 | 0 | 205 |
| Regulatory region variant | 3 | 1 | 273 |
| 5 prime UTR variant | 1 | 0 | 22 |
| Splice region variant | 0 | 0 | 17 |
| Coding sequence variant | 0 | 0 | 1 |
| Stop retained variant | 0 | 0 | 1 |
| Intron variant | 8 | 17 | 2,772 |
| Downstream gene variant | 0 | 7 | 1,106 |
| Splice donor variant | 0 | 0 | 1 |
| NMD transcript variant | 7 | 9 | 1,063 |
| TF binding site variant | 0 | 0 | 6 |
Calls made by all three algorithms are not included in the counts.