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 | 45.7% | 53.7 / 64.9 | 81 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 2,001,918 | 0 | A | C | 32.9% | 154.3 / 37.0 | 82 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,568,504 | 0 | T | G | 30.4% | 280.1 / 28.1 | 139 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 376,401 | 0 | T | G | 29.0% | 119.9 / 13.9 | 62 | L315V (TTG→GTG) | mhpT | 3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| * | NC_000913 | 2,326,450 | 0 | T | G | 28.4% | 166.5 / 43.1 | 81 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 1,550,663 | 0 | A | C | 27.7% | 144.9 / 21.6 | 65 | N68T (AAC→ACC) | fdnH | formate dehydrogenase N subunit beta |
| * | NC_000913 | 650,809 | 0 | T | G | 27.4% | 210.5 / 30.7 | 96 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 4,111,747 | 0 | G | T | 27.3% | 135.5 / 27.1 | 55 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 753,125 | 0 | T | A | 27.1% | 101.4 / 15.7 | 48 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 3,206,435 | 0 | C | T | 26.8% | 71.9 / 17.6 | 41 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 29,496 | 0 | T | A | 26.0% | 100.5 / 20.0 | 50 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 4,429,984 | 0 | T | G | 25.0% | 131.9 / 17.0 | 56 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 646,747 | 0 | T | G | 24.6% | 146.2 / 28.2 | 65 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 1,645,034 | 0 | A | C | 24.2% | 144.3 / 14.2 | 62 | intergenic (‑132/+85) | rem/hokD | Qin prophage; protein Rem/Qin prophage; toxic protein HokD |
| * | NC_000913 | 3,608,719 | 0 | G | A | 22.8% | 120.2 / 12.5 | 57 | intergenic (+70/+32) | zntA/tusA | Zn(2(+))/Cd(2(+))/Pb(2(+)) exporting P‑type ATPase/sulfur transfer protein TusA |
| * | NC_000913 | 1,435,727 | 0 | G | A | 22.5% | 86.7 / 13.1 | 40 | intergenic (‑108/+33) | uspF/ompN | nucleotide binding filament protein/outer membrane porin N |
| * | NC_000913 | 786,855 | 0 | A | C | 22.4% | 149.5 / 12.5 | 58 | G247G (GGT→GGG) | gpmA | 2,3‑bisphosphoglycerate‑dependent phosphoglycerate mutase |
| * | NC_000913 | 1,068,173 | 0 | T | G | 22.1% | 254.9 / 32.3 | 104 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| * | NC_000913 | 4,296,060 | 0 | C | T | 20.5% | 263.1 / 60.3 | 122 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 501,564 | 0 | A | C | 20.0% | 126.1 / 15.1 | 50 | *559E (TAA→GAA) | ybaL | putative transporter YbaL |
| Marginal new junction evidence (lowest skew 10 of 14 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1207805 | 119 (1.120) | 22 (0.240) | 20/244 | 2.8 | 18.7% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 86 (0.920) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 4542682 = | 95 (0.900) | 4 (0.040) | 4/258 | 7.5 | 4.0% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 102 (1.030) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 2817783 = | 132 (1.250) | 3 (0.030) | 3/236 | 7.7 | 2.7% | intergenic (‑280/+1) | yqaB/argQ | fructose‑1‑phosphatase/tRNA‑Arg |
| ? | NC_000913 | = 2817922 | 101 (1.120) | intergenic (‑62/+137) | argQ/argZ | tRNA‑Arg/tRNA‑Arg | |||||
| * | ? | NC_000913 | = 651890 | 125 (1.180) | 3 (0.030) | 3/264 | 8.1 | 2.5% | intergenic (‑34/‑345) | citC/dpiB | citrate lyase synthetase/sensory histidine kinase DpiB |
| ? | NC_000913 | = 651924 | 112 (1.110) | intergenic (‑68/‑311) | citC/dpiB | citrate lyase synthetase/sensory histidine kinase DpiB | |||||
| * | ? | NC_000913 | 226608 = | NA (NA) | 3 (0.030) | 3/262 | 8.1 | NA | noncoding (850/2904 nt) | rrlH | 23S ribosomal RNA |
| ? | NC_000913 | 226686 = | NA (NA) | noncoding (928/2904 nt) | rrlH | 23S ribosomal RNA | |||||
| * | ? | NC_000913 | 3957987 = | 90 (0.850) | 3 (0.030) | 3/270 | 8.2 | 3.2% | coding (18/1476 nt) | ilvC | ketol‑acid reductoisomerase (NADP(+)) |
| ? | NC_000913 | 3958082 = | 94 (0.910) | coding (113/1476 nt) | ilvC | ketol‑acid reductoisomerase (NADP(+)) | |||||
| * | ? | NC_000913 | 1564068 = | 80 (0.760) | 3 (0.030) | 3/270 | 8.2 | 3.7% | coding (1666/2400 nt) | dosP | oxygen‑sensing c‑di‑GMP phosphodiesterase DosP |
| ? | NC_000913 | = 1565424 | 79 (0.760) | coding (310/2400 nt) | dosP | oxygen‑sensing c‑di‑GMP phosphodiesterase DosP | |||||
| * | ? | NC_000913 | 4288195 = | 74 (0.700) | 3 (0.030) +G |
3/274 | 8.3 | 2.7% | coding (432/1437 nt) | nrfA | cytochrome c552 nitrite reductase |
| ? | NC_000913 | = 4556112 | 142 (1.340) | coding (209/831 nt) | yjiC | uncharacterized protein YjiC | |||||
| * | ? | NC_000913 | 4168372 = | 45 (0.430) | 5 (0.050) | 3/272 | 8.3 | 10.1% | noncoding (1/76 nt) | gltT | tRNA‑Glu |
| ? | NC_000913 | = 4169137 | NA (NA) | noncoding (497/2904 nt) | rrlB | 23S ribosomal RNA | |||||
| * | ? | NC_000913 | = 3361300 | 156 (1.470) | 3 (0.030) | 3/274 | 8.3 | 1.7% | coding (125/765 nt) | gltF | periplasmic protein GltF |
| ? | NC_000913 | 3361404 = | 197 (1.880) | coding (229/765 nt) | gltF | periplasmic protein GltF | |||||