Table 2. Single-nucleotide variants associated with mink by genome-wide association studies (GWAS).
“Pos” refers to the nucleotide position in the reference genome. Homoplasy counts in focal animals (cases), humans (controls), and p-values are averaged across replicates in which the site’s family-wise p-values were <0.05. Where applicable, amino acid positions refer to the polyprotein with mature protein positions in parenthesis. The ‘local transmission odds ratio’ is the result of a Fisher’s exact test of the likelihood that the alternate base (animal-associated minor allele) was enriched in the local human population where the mink sequences bearing the alternate base were sampled (Methods). n.s., not significant. Odds ratio p-value: *<0.05, **<0.01, ***<0.001.
| Pos. | Ref. base | Alt. base | Amino acid change | Gene | Homoplasy count in focal animal | Homoplasy count in humans | p-value (pointwise) | p-value (familywise) | Siginificant in N replicates | Local transmission odds ratio |
|---|---|---|---|---|---|---|---|---|---|---|
| 26047 | U | G | L219V | ORF3a | 6 | 0 | 0.0014 | 0.0365 | 10 | 3.93 *** |
| 12795 | G | A | G4177E (nsp9 G37E) |
ORF1ab/pp1ab/nsp9/replicase | 6 | 0 | 0.0015 | 0.0368 | 6 | 7.53 *** |
| 23064 | A | C | N501T | Spike/S1/RBD/binds ACE2 | 6.4 | 0 | 0.0010 | 0.0258 | 5 | 0.48 *** |