TABLE 4.
Mutation pattern of recombined and nonrecombined intervalsa
| Original nucleotide | No. of nucleotides | % (no.) of mutated sequences (10−5) | % (no.) of nucleotide mutations out of total mutations |
|||
|---|---|---|---|---|---|---|
| A | C | G | T | |||
| Recombined interval | ||||||
| A | 111,789 | 8.1 (9) | 0 | 3.7 (2) | 13.0 (7) | 0.0 (0) |
| C | 56,088 | 12.5 (7) | 3.7 (2) | 0 | 1.9 (1) | 7.4 (4) |
| G | 66,473 | 45.1 (30) | 46.3 (25) | 3.7 (2) | 0 | 5.6 (3) |
| T | 63,558 | 12.6 (8) | 5.6 (3) | 5.6 (3) | 3.7 (2) | 0 |
| Nonrecombined interval from recombined sequence | ||||||
| A | 220,054 | 5.0 (11) | 0 | 4.7 (2) | 20.9 (9) | 0.0 (0) |
| C | 101,042 | 4.9 (5) | 0.0 (0) | 0 | 2.3 (1) | 9.3 (4) |
| G | 124,497 | 16.9 (21) | 41.9 (18) | 0.0 (0) | 0 | 7.0 (3) |
| T | 125,032 | 4.8 (6) | 0.0 (0) | 11.6 (5) | 2.3 (1) | 0 |
| Plasmid DNA control | ||||||
| A | 1,892,627 | 4.9 (99) | 0 | 1.1 (4) | 20.8 (76) | 4.4 (16) |
| C | 883,997 | 12.4 (117) | 5.7 (21) | 0 | 2.2 (8) | 20.8 (76) |
| G | 1,074,185 | 11.4 (131) | 25.4 (93) | 0.5 (2) | 0 | 6 (22) |
| T | 1,080,207 | 4.5 (52) | 1.9 (7) | 10.7 (39) | 0.5 (2) | 0 |
a
The frequencies of substitution mutations in A, C, G, and T as well as the nucleotide to which the nucleotide is mutated are indicated for recombined intervals and for nonrecombined intervals from recombined sequences. These mutation patterns are the cumulative product of experimental factors (such as sequencing error) and viral factors. To give some indication of the contribution of sequencing error to the pattern seen, the frequency of substitution mutations in the plasmid DNA control is shown.