Table II. Nonsynonymous SNPs in day 3 samples compared to A/swine/England/1353/2009.
| Sample | Segment | AA Posa | nt Pos | Ref Base | Coverage | AA Change | SNP Type | A Number | T Number | G Number | C Number | N Numberb | Compared with Inoculant |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 30_Naive | KR701097.1_HA | 226 | 676 | A | 271,572 | AAG(K)˗GAG(E) | Nonsyn | Ref = A | T = 45 (0.000) | G = 236,453 (0.871) | C = 81 (0.000) | n = 0 (0.000) | Same as inoculant |
| 31_Naive | KR701097.1_HA | 226 | 676 | A | 190,623 | AAG(K)˗GAG(E) | Nonsyn | Ref = A | T = 95 (0.000) | G = 158,242 (0.830) | C = 43 (0.000) | n = 0 (0.000) | Same as inoculant |
| 51_2–12c | KR701097.1_HA | 226 | 676 | A | 8,398 | AAG(K)˗GAG(E) | Nonsyn | Ref = A | T = 0 (0.000) | G = 8,394 (1.000) | C = 0 (0.000) | n = 0 (0.000) | Same as inoculant |
| 53_2–12c | KR701097.1_HA | 172 | 515 | G | 123,369 | GGA(G)˗GAA(E) | Nonsyn | A = 14,937 (0.121) | T = 6 (0.000) | ref = G | C = 22 (0.000) | n = 0 (0.000) | New SNP |
| KR701097.1_HA | 201 | 602 | C | 151,699 | ACT(T)˗ATT(I) | Nonsyn | A = 14 (0.000) | T = 16,907 (0.111) | G = 67 (0.000) | ref = C | n = 0 (0.000) | New SNP | |
| KR701097.1_HA | 226 | 676 | A | 139,973 | AAG(K)˗GAG(E) | Nonsyn | Ref = A | T = 37 (0.000) | G = 97,706 (0.698) | C = 54 (0.000) | n = 0 (0.000) | Same as inoculant |
a
Amino acid and nucleotide numberings start at Met or ATG.
b
Mixed base calls at that position.
Nonsyn, nonsynonymous; Pos, position; Ref, reference; Syn, synonymous.