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 | 375,146 | 0 | G | A | 42.9% | 1.6 / 21.1 | 21 | intergenic (+265/‑313) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| * | NC_000913 | 29,496 | 0 | T | A | 38.3% | 77.3 / 42.4 | 60 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 4,604,344 | 0 | C | T | 37.2% | 114.5 / 60.7 | 94 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 4,568,504 | 0 | T | G | 35.4% | 207.4 / 28.0 | 128 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 3,206,435 | 0 | C | T | 34.0% | 72.7 / 28.5 | 50 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 2,001,918 | 0 | A | C | 32.1% | 139.7 / 32.7 | 81 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 3,206,444 | 0 | T | A | 31.4% | 83.5 / 19.8 | 51 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,111,747 | 0 | G | T | 29.6% | 134.9 / 22.2 | 54 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 786,855 | 0 | A | C | 28.8% | 104.7 / 10.6 | 52 | G247G (GGT→GGG) | gpmA | 2,3‑bisphosphoglycerate‑dependent phosphoglycerate mutase |
| * | NC_000913 | 4,101,507 | 0 | T | G | 28.8% | 130.6 / 11.2 | 66 | intergenic (+77/‑183) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 2,326,450 | 0 | T | G | 28.6% | 135.2 / 43.1 | 77 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 372,640 | 0 | T | G | 26.2% | 118.0 / 17.1 | 61 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 650,809 | 0 | T | G | 25.4% | 127.9 / 16.0 | 63 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 802,118 | 0 | A | C | 25.0% | 128.9 / 11.9 | 60 | T78P (ACC→CCC) | ybhI | putative tricarboxylate transporter |
| * | NC_000913 | 4,111,752 | 0 | T | C | 24.6% | 142.2 / 13.4 | 69 | K155E (AAA→GAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 4,296,060 | 0 | C | T | 22.7% | 292.9 / 79.3 | 141 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 501,564 | 0 | A | C | 22.6% | 110.4 / 19.8 | 53 | *559E (TAA→GAA) | ybaL | putative transporter YbaL |
| * | NC_000913 | 753,125 | 0 | T | A | 22.6% | 152.1 / 15.1 | 62 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 4,429,984 | 0 | T | G | 21.7% | 133.0 / 14.8 | 60 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 4,223,593 | 0 | T | G | 21.5% | 192.4 / 12.2 | 79 | K12N (AAA→AAC) | iclR | DNA‑binding transcriptional repressor IclR |
| Marginal new junction evidence (lowest skew 10 of 27 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 109 (1.090) | 13 (0.150) | 11/244 | 5.5 | 12.8% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 81 (0.910) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 101 (1.010) | 8 (0.090) | 7/244 | 7.0 | 8.6% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 81 (0.910) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 608007 = | NA (NA) | 7 (0.090) | 5/224 | 7.5 | 9.0% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 609352 = | 71 (0.870) | intergenic (+175/+107) | insL‑2/entD | IS186/IS421 transposase/phosphopantetheinyl transferase EntD | |||||
| * | ? | NC_000913 | 339883 = | NA (NA) | 10 (0.130) | 4/206 | 7.6 | NA | coding (91/297 nt) | yahH | putative uncharacterized protein YahH |
| ? | NC_000913 | 377489 = | NA (NA) | noncoding (34/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 339756 = | NA (NA) | 10 (0.130) | 4/206 | 7.6 | NA | intergenic (+13/‑37) | yahG/yahH | DUF1116 domain‑containing protein YahG/putative uncharacterized protein YahH |
| ? | NC_000913 | 377523 = | NA (NA) | intergenic (+212/+12) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 9 (0.100) | 6/260 | 7.8 | NA | intergenic (+41/‑537) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377329 = | NA (NA) | intergenic (+18/+206) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 4 (0.050) | 3/202 | 8.1 | NA | intergenic (+41/‑537) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377430 = | NA (NA) | intergenic (+119/+105) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 340006 | NA (NA) | 3 (0.040) +29 bp |
3/216 | 8.5 | NA | noncoding (18/29 nt) | other | REPv23f |
| ? | NC_000913 | = 377529 | NA (NA) | intergenic (+218/+6) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 339913 | NA (NA) | 3 (0.040) +29 bp |
3/216 | 8.5 | NA | noncoding (18/29 nt) | other | REPv23d |
| ? | NC_000913 | = 377529 | NA (NA) | intergenic (+218/+6) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 339820 | NA (NA) | 3 (0.040) +29 bp |
3/216 | 8.5 | NA | noncoding (18/29 nt) | other | REPv23b |
| ? | NC_000913 | = 377529 | NA (NA) | intergenic (+218/+6) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||