Table 2
From the following article
High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi
Kathryn E Holt, Julian Parkhill, Camila J Mazzoni, Philippe Roumagnac, François-Xavier Weill, Ian Goodhead, Richard Rance, Stephen Baker, Duncan J Maskell, John Wain, Christiane Dolecek, Mark Achtman & Gordon Dougan
Nature Genetics 40, 987 - 993 (2008) Published online: 27 July 2008
doi:10.1038/ng.195
Table 2. Genetic variation detected in 19 Typhi genomes
| Intrahaplotype | Interhaplotype | Conserved | Total | |
|---|---|---|---|---|
Frequencies of mutations according to age (recent, intrahaplotype; intermediate, interhaplotype; oldest, conserved). Percentages indicate the relative frequencies within each age group, separately for alleles that could be reliably determined for all isolates (complete allele data) and those that could not (incomplete allele data). n.a., not applicable. | ||||
| Deletions | 5 | 8 | 7 | 20 |
| Phage insertions | n.a. | 5 | 4 | 9 |
| Plasmids | 3 | 2 | 0 | 5 |
| SNPs (complete allele data) | 93 | 1,356 | 338 | 1,787 |
| - Intergenic | 6 (6.5%) | 177 (13.1%) | 44 (13.0%) | 227 |
| - Synonymous | 21 (22.6%) | 477 (35.2%) | 106 (31.4%) | 604 |
| - Nonsynonymous | 61 (65.6%) | 663 (48.9%) | 176 (52.1%) | 900 |
| - Nonsense | 5 (5.4%) | 39 (2.9%) | 12 (3.6%) | 56 |
| - dN/dS | 0.98 | 0.46 | 0.52 | 0.49 |
| SNPs (incomplete allele data) | 19 | 122 | 35 | 176 |
| - Intergenic | 4 (21.1%) | 24 (19.7%) | 6 (17.1%) | 34 |
| - Synonymous | 3 (15.8%) | 41 (33.6%) | 12 (34.3%) | 56 |
| - Nonsynonymous | 12 (63.2%) | 57 (46.7%) | 17 (48.6%) | 86 |
| - Nonsense | 0 (0.0%) | 0 (0.0%) | 0 (0.0%) | 0 |
| - dN/dS | 1.24 | 0.44 | 0.44 | 0.48 |
