Table 1.
Nucleotide Changes and Frequencies in Three Adapted Codon-Modified Lines.
| Line (frequencya) |
||||||
|---|---|---|---|---|---|---|
| Position | Base Change | AA Change | Gene (function) | S1 | S2 | L1 |
| 4303 | A →G | k 378 r | 1 (RNAP) | — | 0.115 | — |
| 3664 | A → C | n 165 t | 1 | — | — | 0.214 |
| 9158 | A → T | m 1 mb | 2.5 (ssDNA binding) | — | — | 0.389 |
| 14204 | G → A | g 93 d | 4.7 (DNA metabolism) | — | — | 0.196 |
| 14279 | T → C | i 118 t | 4.7 | — | — | 0.528 |
| 17766 | T → C | v 88 a | 6 (exonuclease) | — | 0.200 | — |
| 23129 | A → G | i 55 v | 10A (major capsid) | 0.438 | 0.114 | — |
| 23131 | A → C | i 55 i | 10A | 0.350 | 0.100 | 0.891 |
| 23425 | T → C | n 153 n | 10A | — | 0.188 | — |
| 23431 | T → C | n 155 n | 10A | — | 0.172 | — |
| 23434 | A → C | i 156 i | 10A | 0.111 | — | — |
| A → G | i 156 m | 10A | — | — | 0.500 | |
| 24088 | G → A | e 375 k | 10B (major capsid) | — | — | 0.720 |
| 24106 | G → A | a 361 t | 10B | — | — | 0.406 |
| 26984 | A → C | t 715 p | 12 (internal virion) | — | — | 0.429 |
| 36052 | A → C | s 477 r | 17 (tail fiber) | — | 0.158 | — |
| 38307 | T → C | l 313 s | 19 (terminase) | — | 0.125 | — |
NOTE.—A polymorphic, silent G → A change in gene 17 (base 35772, codon 383) was observed in all lines at a frequency of ∼0.4 relative to the wild-type base. This change was even observed in the initial T710A0.1 which was recently derived from a clonal isolate. We suspect that this change is a sequencing artefact and omit it from the table and our discussion of evolution in these lines.
a
To be reported here, the frequency of a nucleotide change had to reach 0.1 and be observed in at least two reads.
b
Change to a UUG start codon.