Table 3 Details of single nucleotide polymorphisms (SNPs) detected within the 454 data
Virus | Average depth | Maximum depth | Depth at SNP | % variant | Position (genome) | Gene (Position) | Nuc cons | Nuc variant | AA cons | AA variant | AA residue |
|---|---|---|---|---|---|---|---|---|---|---|---|
Brain tissue samples | |||||||||||
RV437 | 44 | 103 | 60 | 8 | 2768 | M (275) | T | C | Leu | Ser | 92 |
63 | 3 | 2781 | M (288) | T | C | Val | Val | 96 | |||
55 | 51 | 3049 | M (556) | T | C | Leu | Phe | 186 | |||
28 | 18 | 4403 | G (1090) | T | C | Leu | Leu | 364 | |||
28 | 7 | 7855 | L (2451) | C | T | Asn | Asn | 817 | |||
RV2417 | 35.5 | 81 | NA | ||||||||
RV61 | 53.2 | 165 | 34 | 18 | 3503 | G (209) | C | T | Ile | Thr | 70 |
RV2508 | 17 | 53 | 17 | 23 | 9523 | L (4128) | A | G | Ser | Ser | 1376 |
RV2627 | 17.7 | 46 | NA | ||||||||
RV2516 | 16.5 | 43 | NA | ||||||||
RV50 | 8.6 | 16 | 11 | 27 | 11349 | L (5944) | C | G | Asn | Asp | 1982 |
RV2772 | 14.5 | 31 | 13 | 38 | 1293 | N (1223) | A | G | Lys | Arg | 408 |
22 | 5 | 8179 | L (2771) | T | A | Phe | Tyr | 924 | |||
Cultured virus samples | |||||||||||
RV2324 | 65 | 272 | 47 | 11 | 3490 | G (175) | G | A | Glu | Lys | 59 |
47 | 21 | 3491 | G (176) | A | G | Glu | Gly | 59 | |||
42 | 31 | 3711 | G (396) | C | A | His | Gln | 132 | |||
44 | 25 | 4103 | G (788) | A | G | Gln | Arg | 263 | |||
36 | 11 | 8376 | L (2967) | C | T | Asp | Asp | 989 | |||
RV1787 combined | 4.3 | 11 | 4 | 25 | 2679 | M (170) | G | A | Gly | Glu | 57 |
RV20 combined | 156 | 277 | 107 | 2 | 346 | N (276) | C | A/T | Tyr | */Tyr | 92 |
87 | 2 | 1621 | P (105) | T | C | Ser | Ser | 35 | |||
81 | 2 | 1669 | P (153) | G | A | Glu | Glu | 51 | |||
77 | 3 | 1710 | P (194) | A | T | Gln | Leu | 65 | |||
93 | 39 | 3143 | M-G (NA) | C | T | NA | NA | NA | |||
103 | 2 | 3671 | G (356) | G | A | Trp | * | 119 | |||
96 | 2 | 4403 | G (1087) | T | C | Cys | Arg | 363 | |||
94 | 37 | 4584 | G (1268) | T | C | Met | Thr | 423 | |||
95 | 2 | 6217 | L (766) | T | C | Ser | Pro | 256 | |||
134 | 1 | 7910 | L (2459) | T | C | Ile | Thr | 820 | |||
107 | 2 | 8244 | L (2793) | C | A | Ser | Arg | 931 | |||
106 | 2 | 8473 | L (3022) | A | G | Thr | Ala | 1008 | |||