Table 2. Functional classification and novelty status of the detected single nucleotide polymorphisms (SNPs) and insertion–deletions (InDels).
| SNPs | InDels | ||
| 3 prime UTR variant | 20,704 | 3 prime UTR variant | 2,533 |
| 5 prime UTR variant | 3,838 | 5 prime UTR variant | 288 |
| coding sequence variant | 50 | INTERGENIC | 707,901 |
| downstream gene varianta | 309,055 | coding sequence variant | 86 |
| initiator codon variant | 76 | downstream gene variant | 33,854 |
| intergenic variant | 7,034,568 | frameshift variant | 859 |
| intron variant | 2,669,278 | inframe deletion | 231 |
| mature miRNA variant | 59 | inframe insertion | 150 |
| missense variant | 31,503 | intron variant | 279,622 |
| nc transcript variant | 15 | mature miRNA variant | 31 |
| non coding exon variant | 3,362 | missense variant | 29 |
| splice acceptor variant | 189 | nc transcript variant | 20 |
| splice donor variant | 175 | non coding exon variant | 213 |
| splice region variant | 6,504 | splice acceptor variant | 56 |
| stop gained | 328 | splice donor variant | 44 |
| stop lost | 20 | splice region variant | 667 |
| stop retained variant | 32 | stop gained | 1 |
| synonymous variant | 40,878 | upstream gene variant | 36,682 |
| upstream gene variant | 350,544 | ||
| fully known | 4,803,811 | fully known | 224,125 |
| novel | 5,667,367 | novel | 839,142 |
| Total | 10,471,178 | Total | 1,063,267 |
Abbreviations: UTR, untranslated region; nc, non-coding.
a
'Downstream gene variant' indicates variants within 5 kb downstream of the 3' end of a transcript.