Table 1.
Number of SNPs and Indels in sequence ontology classes annotated using the VEP software
| Sequence ontology class | SNP | Indel |
|---|---|---|
| splice_acceptor_variant | 272 | 84 |
| splice_donor_variant | 273 | 71 |
| stop_gained | 580 | 16 |
| frameshift_variant | 0 | 1324 |
| stop_lost | 33 | 0 |
| start_lost | 106 | 4 |
| inframe_insertion | 0 | 290 |
| inframe_deletion | 0 | 440 |
| missense_variant | 47,429 | 0 |
| protein_altering_variant | 0 | 12 |
| splice_region_variant | 9553 | 1059 |
| stop_retained_variant | 45 | 2 |
| synonymous_variant | 58,387 | 0 |
| coding_sequence_variant | 166 | 125 |
| mature_miRNA_variant | 83 | 23 |
| 5_prime_UTR_variant | 6744 | 600 |
| 3_prime_UTR_variant | 30,716 | 4074 |
| non_coding_transcript_exon_variant | 6296 | 434 |
| intron_variant | 3,960,673 | 422,764 |
| non_coding_transcript_variant | 24 | 25 |
| upstream_gene_variant | 526,000 | 56,715 |
| downstream_gene_variant | 454,753 | 51,672 |
| intergenic_variant | 10,620,678 | 1,041,144 |
| Total | 15,722,811 | 1,580,878 |