Table 1. Dataset statistics and SNP prediction summary.
Bacterial clone (C) and mixed-population samples (M) from different generations of the Ara-1 population of the long-term E. coli evolution experiment were sequenced on Genome Analyzer systems. Each dataset had the specified number of positions with coverage only from reads with unique best matches to the ancestral genome; mean (μ) and index of dispersion (σ2/μ) for the distribution of read coverage depth at these unique-only positions; and number of base mismatch errors in reads with a unique best alignment to the ancestral genome. The numbers of SNPs predicted by our procedure using a E–value cutoff of one and after further filtering out predictions with biased base quality score and strand distributions are also reported for each sample. Ratios of non-synonymous to synonymous substitutions are shown in parentheses.
| Sample | Unique-only positions |
Coverage | Base errors |
SNP predictions (dN/dS) | ||||
|---|---|---|---|---|---|---|---|---|
| μ | σ2/μ | E-value ≤ 1 | Bias filtered | |||||
| clone samples | ||||||||
| C0K | 4,475,960 | 40.2 | 3.1 | 1,282,378 | 22 | (17/3) | 8 | (6/2) |
| C2K | 4,469,732 | 45.1 | 3.2 | 1,332,415 | 29 | (18/5) | 5 | (3/0) |
| C5K | 4,468,358 | 53.5 | 3.6 | 1,497,884 | 38 | (25/9) | 7 | (4/3) |
| C10K | 4,441,204 | 51.8 | 3.3 | 1,366,094 | 47 | (37/4) | 5 | (5/0) |
| C15K | 4,442,023 | 52.3 | 3.4 | 1,248,779 | 51 | (38/11) | 2 | (1/1) |
| C20K | 4,441,245 | 48.0 | 3.2 | 1,252,909 | 42 | (30/9) | 7 | (5/1) |
| C40K | 4,411,765 | 53.8 | 3.4 | 1,394,982 | 53 | (33/13) | 8 | (4/2) |
| mixed-population samples | ||||||||
| M2K | 4,476,202 | 54.2 | 4.1 | 702,687 | 59 | (51/3) | 7 | (7/0) |
| M5K | 4,476,629 | 56.7 | 3.6 | 716,580 | 70 | (46/10) | 5 | (4/1) |
| M10K | 4,465,577 | 57.4 | 4.3 | 688,297 | 117 | (71/25) | 20 | (10/1) |
| M15K | 4,469,198 | 58.7 | 4.2 | 667,182 | 115 | (72/24) | 19 | (12/0) |
| M20K | 4,443,151 | 40.6 | 4.4 | 776,788 | 34 | (22/3) | 6 | (4/1) |
| M30K | 4,444,156 | 52.1 | 4.5 | 720,115 | 415 | (314/50) | 364 | (270/46) |
| M40K | 4,449,187 | 58.3 | 5.5 | 611,554 | 1150 | (817/167) | 1062 | (754/148) |