Table 2.
Functional annotation of variants identified in father, daughter, and cat. Variants with MAF >0.7 in at least one sample are shown. NA, not assigned allele frequencies due to low coverage (<10×). Coverage, number of high-quality reads with mapping quality >20.
| Position | Annotation | Allele frequency |
Coverage |
||||
|---|---|---|---|---|---|---|---|
| Cat | Father | Daughter | Cat | Father | Daughter | ||
| 241 | 5’UTR:nc.C241T,NA,NA; | 1 | 0.99 | 0.99 | 11,613 | 12,446 | 11,923 |
| 913 | orf1ab:c.648C > T,p.S216S,synonymous;nsp2:c.108C > T,p.S36S,synonymous; | 0.93 | 0.94 | 0.94 | 11,407 | 1783 | 519 |
| 3037 | orf1ab:c.2772C > T,p.F924F,synonymous;nsp3:c.318C > T,p.F106F,synonymous; | 0.99 | 0.99 | 0.99 | 1948 | 2097 | 1635 |
| 3267 | orf1ab:c.3002C > T,p.T1001I,missense;nsp3:c.548C > T,p.T183I,missense; | 0.92 | 0.93 | 0.72 | 2924 | 561 | 134 |
| 5388 | orf1ab:c.5123C > A,p.A1708D,missense;nsp3:c.2669C > A,p.A890D,missense; | 0.9 | 0.73 | 0.75 | 96 | 114 | 44 |
| 5986 | orf1ab:c.5721C > T,p.F1907F,synonymous;nsp3:c.3267C > T,p.F1089F,synonymous; | 0.8 | 0.81 | 0.6 | 225 | 289 | 163 |
| 11,288 | orf1ab:c.11023TCTGGTTTT > .........,p.SGF3675-,inframeDel;nsp6:c.316TCTGGTTTT > .........,p.SGF106-,inframeDel; | 0.94 | 0.98 | 0.93 | 3405 | 6662 | 2896 |
| 11,451 | orf1ab:c.11186A > G,p.Q3729R,missense;nsp6:c.479A > G,p.Q160R,missense; | 0 | NA | 1 | 853 | 6 | 69 |
| 14,408 | orf1ab:c.14144C > T,p.P4715L,missense;nsp12:c.968C > T,p.P323L,missense; | 1 | 1 | NA | 43 | 78 | 0 |
| 14,676 | orf1ab:c.14412C > T,p.P4804P,synonymous;nsp12:c.1236C > T,p.P412P,synonymous; | 0.95 | 1 | NA | 19 | 20 | 1 |
| 15,279 | orf1ab:c.15015C > T,p.H5005H,synonymous;nsp12:c.1839C > T,p.H613H,synonymous; | 0.94 | 0.92 | 0.94 | 81,871 | 10,882 | 1803 |
| 16,176 | orf1ab:c.15912 T > C,p.T5304T,synonymous;nsp12:c.2736 T > C,p.T912T,synonymous; | 0.81 | 0.66 | 0.8 | 270 | 362 | 201 |
| 21,765 | spike:c.203TACATG > ......,p.IHV68I,inframeDel; | 0.74 | 0.66 | 0.89 | 176 | 140 | 56 |
| 21,993 | spike:c.431ATT > …,p.YY144Y,inframeDel; | 0.91 | 0.94 | 1 | 350 | 191 | 72 |
| 23,063 | spike:c.1501A > T,p.N501Y,missense; | 0.92 | 0.98 | 0.94 | 59,839 | 92,889 | 73,230 |
| 23,271 | spike:c.1709C > A,p.A570D,missense; | 0.94 | 1 | NA | 235 | 187 | 6 |
| 23,403 | spike:c.1841A > G,p.D614G,missense; | 1 | 1 | 1 | 164 | 214 | 98 |
| 23,604 | spike:c.2042C > A,p.P681H,missense; | 0.66 | 0.78 | 0.87 | 2906 | 924 | 457 |
| 23,709 | spike:c.2147C > T,p.T716I,missense; | 0.73 | 0.63 | 0.78 | 995 | 1197 | 632 |
| 24,914 | spike:c.3352G > C,p.D1118H,missense; | 0.93 | 0.97 | 0.79 | 252 | 110 | 38 |
| 27,972 | orf8:c.79C > T,p.Q27*,stopGain; | 0.95 | 0.99 | 0.96 | 65,155 | 8235 | 5423 |
| 28,048 | orf8:c.155G > T,p.R52I,missense; | 0.95 | 0.99 | 0.94 | 32,546 | 4154 | 2774 |
| 28,273 | NA | 0.97 | 0.96 | 0.85 | 6187 | 3072 | 377 |
| 28,280 | geneN:c.7GAT > CTA,p.D3L,missense; | 0.97 | 0.97 | 0.88 | 6180 | 3047 | 366 |
| 28,881 | geneN:c.608GGG > AAC,p.RG203KR,missense; | 0.92 | 0.91 | 0.8 | 6842 | 11,609 | 7074 |
| 28,977 | geneN:c.704C > T,p.S235F,missense; | 0.97 | 0.99 | 0.92 | 21,515 | 8684 | 658 |