mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,604,344 | 0 | C | T | 43.1% | 117.9 / 102.0 | 137 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 1,825,061 | 0 | G | A | 38.5% | 64.6 / 28.5 | 52 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 4,111,747 | 0 | G | T | 33.3% | 141.0 / 43.8 | 66 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 3,556,205 | 0 | A | C | 31.6% | 144.8 / 24.7 | 79 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 3,556,207 | 0 | T | C | 31.6% | 126.8 / 27.3 | 76 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 2,001,918 | 0 | A | C | 29.8% | 181.9 / 37.4 | 94 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 29,496 | 0 | T | A | 28.6% | 155.1 / 35.3 | 77 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 650,809 | 0 | T | G | 27.3% | 226.2 / 32.9 | 110 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 4,568,504 | 0 | T | G | 26.0% | 315.6 / 22.0 | 153 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 1,775,467 | 0 | A | C | 25.0% | 149.7 / 10.6 | 72 | intergenic (+23/‑120) | aroD/ydiF | 3‑dehydroquinate dehydratase/putative acetate‑CoA transferase |
| * | NC_000913 | 3,206,435 | 0 | C | T | 25.0% | 126.6 / 27.3 | 64 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 753,125 | 0 | T | A | 24.0% | 230.3 / 30.1 | 100 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 3,206,444 | 0 | T | A | 23.8% | 137.9 / 15.0 | 63 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 2,326,450 | 0 | T | G | 22.6% | 239.7 / 45.8 | 106 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 753,114 | 0 | G | T | 22.4% | 300.3 / 18.9 | 107 | intergenic (‑319/+71) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 3,926,366 | 0 | A | C | 21.9% | 293.2 / 20.7 | 119 | G30G (GGT→GGG) | mioC | flavoprotein MioC |
| * | NC_000913 | 742,106 | 0 | A | C | 21.4% | 166.3 / 14.2 | 70 | S151A (TCT→GCT) | dtpD | dipeptide:H(+) symporter DtpD |
| * | NC_000913 | 4,101,507 | 0 | T | G | 21.1% | 277.2 / 10.8 | 109 | intergenic (+77/‑183) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 372,640 | 0 | T | G | 21.0% | 198.5 / 14.8 | 81 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 3,240,985 | 0 | T | G | 20.7% | 195.4 / 15.2 | 82 | S348A (TCT→GCT) | sstT | serine/threonine:Na(+) symporter |
| Marginal new junction evidence (lowest skew 10 of 21 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 4542682 = | 97 (0.720) | 19 (0.150) | 15/258 | 5.7 | 18.8% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 74 (0.590) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 250706 = | 116 (0.870) | 4 (0.030) | 4/254 | 9.9 | 3.0% | pseudogene (635/756 nt) | lafU | flagellar system protein, promoterless fragment |
| ? | NC_000913 | 250755 = | 156 (1.270) | pseudogene (684/756 nt) | lafU | flagellar system protein, promoterless fragment | |||||
| * | ? | NC_000913 | 3777891 = | 117 (0.870) | 4 (0.030) | 4/256 | 10.0 | 3.0% | coding (493/1656 nt) | lldP | lactate/glycolate:H(+) symporter LldP |
| ? | NC_000913 | 3778056 = | 147 (1.180) | coding (658/1656 nt) | lldP | lactate/glycolate:H(+) symporter LldP | |||||
| * | ? | NC_000913 | 2996360 = | NA (NA) | 4 (0.030) +C |
4/274 | 10.4 | NA | pseudogene (1/399 nt) | ygeO | putative uncharacterized protein YgeO |
| ? | NC_000913 | = 2997691 | NA (NA) | noncoding (1/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 2068941 = | NA (NA) | 8 (0.060) | 4/276 | 10.4 | NA | noncoding (1331/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 2070273 | NA (NA) | intergenic (‑93/‑4) | insC‑3/yoeA | CP4‑44 prophage; IS2 insertion element repressor InsA/CP4‑44 prophage; TonB‑dependent receptor plug domain‑containing protein YoeA | |||||
| * | ? | NC_000913 | = 3365172 | 366 (2.880) | 9 (0.070) +AGGAG |
3/252 | 10.5 | 2.4% | coding (2366/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3365173 = | 386 (2.880) | coding (2367/2382 nt) | yhcD | putative fimbrial usher protein YhcD | |||||
| * | ? | NC_000913 | 105361 = | 95 (0.710) | 3 (0.020) | 3/252 | 10.5 | 3.3% | coding (57/1152 nt) | ftsZ | cell division protein FtsZ |
| ? | NC_000913 | = 105357 | 88 (0.720) | coding (53/1152 nt) | ftsZ | cell division protein FtsZ | |||||
| * | ? | NC_000913 | = 1286727 | 89 (0.660) | 3 (0.020) | 3/256 | 10.6 | 3.3% | coding (19/276 nt) | ychS | putative uncharacterized protein YchS |
| ? | NC_000913 | = 1286996 | 96 (0.770) | intergenic (+12/+70) | ychS/rttR | putative uncharacterized protein YchS/small RNA RttR | |||||
| * | ? | NC_000913 | 3751076 = | 168 (1.250) | 4 (0.030) | 3/260 | 10.7 | 2.3% | intergenic (+295/+52) | sgbE/yiaT | L‑ribulose‑5‑phosphate 4‑epimerase SgbE/outer membrane protein YiaT |
| ? | NC_000913 | 3751161 = | 184 (1.460) | coding (708/741 nt) | yiaT | outer membrane protein YiaT | |||||
| * | ? | NC_000913 | = 2370736 | 118 (0.880) | 3 (0.020) | 3/262 | 10.8 | 2.6% | coding (719/891 nt) | arnD | putative 4‑deoxy‑4‑formamido‑L‑arabinose‑phosphoundecaprenol deformylase ArnD |
| ? | NC_000913 | = 2370768 | 109 (0.860) | coding (751/891 nt) | arnD | putative 4‑deoxy‑4‑formamido‑L‑arabinose‑phosphoundecaprenol deformylase ArnD | |||||