Table 5 Annotation of variants by functional class
Functional class | SNP | Indel |
|---|---|---|
Intergenic | 7,345,721 (68.0) | 866,042 (66.9) |
Intronic | 2,656,868 (24.6) | 334,542 (25.8) |
Upstream | 367,709 (3.4) | 46,226 (3.6) |
Downstream | 317,069 (2.9) | 41,330 (3.2) |
3′ UTR | 19,677 (0.2) | 3150 (0.2) |
5′ UTR | 4364 (0.0) | 453 (0.0) |
Splice regiona | 6393 (0.1) | 896 (0.1) |
Splice donorb | 230 (0.0) | 53 (0.0) |
Splice acceptorc | 218 (0.0) | 82 (0.0) |
Initiator codond | 74 (0.0) | 1 (0.0) |
Stop gain | 395 (0.0) | - |
Frameshift | - | 1302 (0.1) |
Missense | 34,183 (0.3) | 44 (0.0) |
Synonymous | 40,055 (0.4) | - |
Coding sequencee | 125 (0.0) | 135 (0.0) |
Inframe deletion | - | 261 (0.0) |
Inframe insertion | - | 194 (0.0) |
Stop lost | 29 (0.0) | - |
Stop retained | 25 (0.0) | - |
Within non coding exonf | 3569 (0.0) | 270 (0.0) |
Within mature miRNA | 70 (0.0) | 29 (0.0) |
Nc transcriptf | 20 (0.0) | 26 (0.0) |
Total | 10,796,794 (100.0) | 1,295,036 (100.0) |