Table 3. Single-nucleotide variants associated with deer 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. IG, Intergenic. 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 deer 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) | Significant in N replicates | Local transmission odds ratio |
|---|---|---|---|---|---|---|---|---|---|---|
| 7303 | C | U | I2346I (nsp3 I1524I) |
ORF1a/pp1ab/pp1a/nsp3 | 17.8 | 1.2 | 9.99E-06 | 9.99E-06 | 10 | 2.51*** |
| 9430 | C | U | I3055I (nsp4 I292I) |
ORF1a/pp1ab/pp1a/nsp4 | 15.2 | 6.2 | 9.99E-06 | 9.99E-06 | 10 | 2.20*** |
| 14960 | A | U | N4899I (nsp12 N507I) |
ORF1ab/pp1ab/nsp12/RdRp | 7.8 | 0.1 | 9.99E-06 | 1.09E-05 | 10 | 0** |
| 20259 | C | U | F6665F (nsp15 F213F) |
ORF1ab/pp1ab/nsp15 | 4.8 | 0.1 | 3.39E-05 | 0.0013 | 10 | n.s. |
| 28016 | C | U | F41F | ORF8 | 4 | 0 | 7.59E-05 | 0.0061 | 10 | 6.09*** |
| 12073 | C | U | D3936D (nsp7 D67D) |
ORF1a/pp1ab/pp1a/nsp7 | 5.2 | 1.1 | 4.29E-05 | 0.0025 | 10 | n.s. |
| 29679 | C | U | IG | 3’UTR | 5 | 1.8 | 8.59E-05 | 0.0055 | 10 | 3.17*** |
| 5184 | C | U | P1640L (nsp3 P822L) |
ORF1a/pp1ab/pp1a/nsp3 | 4.6 | 1.6 | 0.0002 | 0.0115 | 8 | 2.61*** |
| 29750 | C | U | IG | 3’UTR/S2M | 5 | 2.6 | 0.0002 | 0.0103 | 7 | 3.12*** |
| 7318 | C | U | F2351F (nsp3 F1533F) |
ORF1a/pp1ab/pp1a/nsp3 | 4 | 0.3 | 0.0001 | 0.0114 | 6 | 3.80*** |
| 16466 | C | U | P5401L (nsp13 P77L) |
ORF1ab/pp1ab/nsp13/Hel | 5 | 1 | 4.99E-05 | 0.0019 | 5 | 4.09*** |
| 7267 | C | U | F2334F (nsp3 F1516F) |
ORF1a/pp1ab/pp1a/nsp3 | 4.4 | 0.8 | 9.39E-05 | 0.0079 | 5 | 2.79*** |
| 210 | G | U | IG | 5’UTR/SL5a | 4 | 0.5 | 0.0001 | 0.0136 | 4 | 3.98*** |
| 6730 | C | U | N2155N (nsp3 N1337N) |
ORF1a/pp1ab/pp1a/nsp3 | 4 | 0.75 | 0.0002 | 0.0168 | 4 | 1.81** |
| 27752 | C | U | T120I | ORF7a | 4 | 0.75 | 0.0002 | 0.0169 | 4 | 4.03*** |
| 11152 | C | U | V3629V (nsp6 V60V) |
ORF1a/pp1ab/pp1a/nsp6 | 4 | 0.7 | 0.0002 | 0.0153 | 3 | 0.80** |
| 5822 | C | U | L1853F (nsp3 L1035F) |
ORF1a/pp1ab/pp1a/nsp3 | 4 | 0.5 | 0.0001 | 0.0118 | 2 | n.s. |
| 9711 | C | U | S3149F (nsp4 S386F) |
ORF1a/pp1ab/pp1a/nsp4 | 4 | 0.5 | 8.49E-05 | 0.0118 | 2 | 0.56** |
| 9679 | C | U | F3138F (nsp4 F375F) | ORF1a/pp1ab/pp1a/nsp4 | 4 | 0 | 9.49E-05 | 0.0067 | 2 | 2.32*** |
| 7029 | C | U | S2255F (nsp3 S1437F) |
ORF1a/pp1ab/pp1a/nsp3 | 4 | 0.5 | 0.0002 | 0.0149 | 2 | 0.22*** |
| 29738 | C | A | IG | 3’UTR/S2M | 4 | 0 | 3.99E-05 | 0.0059 | 1 | n.s. |
| 26767 | U | C | I82T | ORF5/M | 4 | 0 | 8.99E-05 | 0.0057 | 1 | 4.09*** |
| 203 | C | U | IG | 5’UTR/SL5a | 4 | 1 | 0.0003 | 0.0191 | 1 | 5.94*** |
| 12820 | A | G | L4185L (nsp9 L45L) |
ORF1a/pp1ab/pp1a/nsp9 | 5 | 1 | 3.99E-05 | 0.0009 | 1 | 4.52*** |
| 4540 | C | U | Y1425Y (nsp3 Y607Y) |
ORF1a/pp1ab/pp1a/nsp3 | 4 | 1 | 0.0002 | 0.0239 | 1 | 2.80*** |
| 29666 | C | U | L37F | ORF10 | 4 | 1 | 0.0002 | 0.0219 | 1 | 1.54*** |