mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.29.0 revision 8f9c342918e4
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 900 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 3,350,853 | 0 | A | C | 47.9% | 145.0 / 22.8 | 96 | S725A (TCA→GCA) | arcB | aerobic respiration control sensor histidine protein kinase, cognate to two‑component response regulators ArcA and RssB |
| * | NC_000913 | 3,350,844 | 0 | A | C | 46.6% | 149.3 / 17.8 | 88 | L728V (TTA→GTA) | arcB | aerobic respiration control sensor histidine protein kinase, cognate to two‑component response regulators ArcA and RssB |
| * | NC_000913 | 357,890 | 0 | C | A | 46.4% | 55.5 / 44.4 | 71 | L267F (TTG→TTT) | cynR | transcriptional activator of cyn operon; autorepressor |
| * | NC_000913 | 345,328 | 0 | C | A | 46.1% | 142.3 / 58.3 | 102 | intergenic (+337/‑76) | yahL/yahM | uncharacterized protein/uncharacterized protein |
| * | NC_000913 | 941,713 | 0 | T | G | 45.9% | 117.6 / 44.0 | 85 | V252G (GTG→GGG) | dmsA | dimethyl sulfoxide reductase, anaerobic, subunit A |
| * | NC_000913 | 2,326,450 | 0 | T | G | 45.2% | 120.0 / 18.2 | 73 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 29,486 | 0 | C | A | 45.0% | 118.2 / 47.1 | 80 | intergenic (+291/‑165) | dapB/carA | dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase |
| * | NC_000913 | 599,576 | 0 | T | G | 44.7% | 139.1 / 35.5 | 85 | V288G (GTG→GGG) | cusA | copper/silver efflux system, membrane component |
| * | NC_000913 | 1,222,233 | 0 | G | A | 44.4% | 105.1 / 34.7 | 81 | pseudogene (60/75 nt) | ycgH | pseudogene; putative ATP‑binding component of a transport system |
| * | NC_000913 | 213,341 | 0 | A | G | 43.9% | 160.6 / 31.8 | 107 | G337G (GGA→GGG) | tilS | tRNA(Ile)‑lysidine synthetase |
| * | NC_000913 | 357,875 | 0 | A | T | 43.7% | 104.2 / 35.6 | 71 | N272K (AAT→AAA) | cynR | transcriptional activator of cyn operon; autorepressor |
| * | NC_000913 | 357,880 | 0 | T | C | 43.5% | 104.1 / 17.1 | 70 | K271E (AAA→GAA) | cynR | transcriptional activator of cyn operon; autorepressor |
| * | NC_000913 | 1,825,056 | 0 | G | A | 43.2% | 127.1 / 53.5 | 95 | intergenic (‑119/+84) | ves/spy | cold‑ and stress‑inducible protein/periplasmic ATP‑independent protein refolding chaperone, stress‑induced |
| * | NC_000913 | 436,516 | 0 | C | A | 42.9% | 102.9 / 37.3 | 77 | Q295K (CAA→AAA) | thiL | thiamine monophosphate kinase |
| * | NC_000913 | 3,026,941 | 0 | A | C | 42.6% | 166.8 / 29.2 | 101 | E392D (GAA→GAC) | guaD | guanine deaminase |
| * | NC_000913 | 4,536,197 | 0 | A | T | 42.3% | 117.6 / 81.3 | 97 | intergenic (+166/+417) | yjhR/nanS | pseudogene, helicase family; putative frameshift suppressor/9‑O‑acetyl N‑acetylneuraminic acid esterase |
| * | NC_000913 | 907,602 | 0 | A | C | 42.0% | 140.1 / 14.9 | 82 | G227G (GGT→GGG) | ybjT | putative NAD‑dependent oxidoreductase |
| * | NC_000913 | 3,511,923 | 0 | A | C | 41.8% | 217.1 / 12.4 | 110 | V141G (GTT→GGT) | yhfZ | putative DNA‑binding transcriptional regulator |
| * | NC_000913 | 2,151,589 | 0 | A | T | 41.4% | 89.8 / 40.0 | 70 | L135F (TTA→TTT) | yegJ | uncharacterized protein |
| * | NC_000913 | 3,717,014 | 0 | T | G | 41.3% | 197.6 / 24.8 | 104 | G156G (GGT→GGG) | yiaD | multicopy suppressor of bamB; outer membrane lipoprotein |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 925901 = | 93 (0.880) | 15 (0.140) +C |
10/296 | 14.2 | 16.0% | noncoding (71/88 nt) | serW | tRNA‑Ser |
| ? | NC_000913 | = 1097399 | 66 (0.620) | intergenic (+570/+166) | ycdU/serX | putative inner membrane protein/tRNA‑Ser | |||||
| * | ? | NC_000913 | 4542682 = | 142 (1.340) | 8 (0.080) | 8/280 | 14.7 | 6.1% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | 4542996 = | 111 (1.120) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | = 4542690 | 137 (1.290) | 7 (0.070) | 7/280 | 15.4 | 5.5% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | = 4542986 | 110 (1.110) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | = 4398113 | 82 (0.820) | 14 (0.140) +ACGCT |
4/270 | 17.2 | 13.9% | coding (702/1848 nt) | mutL | methyl‑directed mismatch repair protein |
| ? | NC_000913 | 4398114 = | 92 (0.870) | coding (703/1848 nt) | mutL | methyl‑directed mismatch repair protein | |||||
| * | ? | NC_000913 | 59221 = | 116 (1.100) | 29 (0.270) | 4/298 | 18.4 | 20.0% | pseudogene (170/228 nt) | yabP | pseudogene, pentapeptide repeats‑containing |
| ? | NC_000913 | 273955 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||