Table 3.
WGS variants Identified in 30x Coverage of a Persian Cat PRA Trio
| Analysis typeb | |||||
|---|---|---|---|---|---|
| Variant impacta | Functional Class | WGS trio | Trio Segregation | RetNet genes | GWAS haplotype |
| High | Stop gain | 379 | 11 | 6 | 1 |
| Start/Stop loss | 85 | 5 | 2 | - | |
| Splice donor/acceptor | 1262 | 9 | 9 | 1 | |
| Exon deletion | 2 | - | - | - | |
| Frameshift | 2254 | 18 | 20 | 4 | |
| Rare amino acid | - | - | - | - | |
| Moderate | Codon alteration | 971 | 15 | 11 | 4 |
| Missense | 35,444 | 1014 | 544 | 41 | |
| Splice branch | - | - | - | - | |
| 5′ or 3′ UTR Deletion | 1 | - | - | - | |
| Low | 64,791 | 2072 | 1155 | 105 | |
| Modifier | 16,876,221 | 538,148 | 87,816 | 11,018 |
aImpact determined by snpEff as defined by http://snpeff.sourceforge.net/SnpEff_manual.html#eff. b The analyses is based on feline reference genome sequence (V6.2). Effect counts are higher than variant counts because they include the effects of each alternate allele on each nearby gene isoform. GWAS haplotype are the variants identified within the haplotype region. For Trio Segregation, the variants segregated with the disease phenotype as well, not just parent to offspring