Table 2 Predicted variant type reported by SnpEff and Ensembl-VEP for each predicted genetic burden variant.
From: Predicted genetic burden and frequency of phenotype-associated variants in the horse
SnpEff | Ensembl-VEP | Count |
|---|---|---|
Variant types with agreement between SnpEff and Ensembl-VEP | ||
Frameshift | Frameshift | 15,999 |
Splice acceptor | Splice acceptor | 1800 |
Splice donor | Splice donor | 2066 |
Start lost | Start lost | 277 |
Stop gained | Stop gained | 2685 |
Stop lost | Stop lost | 171 |
Transcript ablation | Transcript ablation | 2 |
Total | 23,000 | |
Variant types without agreement between SnpEff and Ensembl-VEP | ||
Exon loss | Frameshift | 3 |
Inframe deletion | 1 | |
Splice acceptor | 11 | |
Splice donor | 25 | |
Frameshift | Inframe deletion | 13 |
Inframe insertion | 3 | |
Protein altering | 2 | |
Splice acceptor | 537 | |
Splice donor | 765 | |
Start lost | 10 | |
Stop gained | 256 | |
Stop lost | 5 | |
Gene fusion | Frameshift | 2 |
Inframe deletion | 1 | |
Splice acceptor | 2 | |
Splice donor | 1 | |
Inframe deletion | Splice acceptor | 10 |
Splice donor | 5 | |
Start lost | 4 | |
Stop lost | 1 | |
Inframe insertion | Frameshift | 1 |
Missense | Splice acceptor | 2 |
Splice donor | 1 | |
Start lost | 34 | |
Splice acceptor | Frameshift | 103 |
Inframe deletion | 3 | |
Inframe insertion | 64 | |
Missense | 14 | |
Protein altering | 6 | |
Splice donor | 404 | |
Stop gained | 40 | |
Splice donor | Frameshift | 374 |
Inframe insertion | 157 | |
Missense | 26 | |
Protein altering | 6 | |
Stop gained | 7 | |
Start lost | Missense | 15 |
Stop gained | Missense | 20 |
Splice acceptor | 1 | |
Splice donor | 1 | |
Stop lost | Missense | 5 |
Splice acceptor | 3 | |
Total | 2944 | |
