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 | |||
NA = not applicable as no SNPs were observed. * stop codon.