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 (highest frequency 20 of 230 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 739,571 | 0 | C | G | 54.5% | 4.2 / 47.0 | 33 | A22G (GCC→GGC) | phr | deoxyribodipyrimidine photolyase |
| * | NC_000913 | 1,877,172 | 0 | A | C | 51.5% | 144.8 / 254.1 | 169 | K88N (AAA→AAC) | yeaO | DUF488 domain‑containing protein YeaO |
| * | NC_000913 | 2,595,081 | 0 | A | C | 50.9% | 75.0 / 166.1 | 108 | V260G (GTG→GGG) | tmcA | tRNA(Met) cytidine acetyltransferase |
| * | NC_000913 | 4,568,504 | 0 | T | G | 45.2% | 590.7 / 269.6 | 384 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 1,150,288 | 0 | C | G | 42.5% | 41.9 / 22.8 | 40 | G187G (GGC→GGG) | fabD | [acyl‑carrier‑protein] S‑malonyltransferase |
| * | NC_000913 | 1,632,523 | 0 | A | C | 41.3% | 760.3 / 246.8 | 492 | intergenic (‑238/‑367) | ydfJ/ynfT | putative transporter YdfJ/protein YnfT |
| * | NC_000913 | 1,678,263 | 0 | T | G | 38.9% | 790.1 / 247.4 | 419 | intergenic (‑360/‑164) | pntA/ydgH | pyridine nucleotide transhydrogenase subunit alpha/DUF1471 domain‑containing protein YdgH |
| * | NC_000913 | 2,840,748 | 0 | G | C | 38.9% | 37.6 / 20.4 | 36 | A409P (GCC→CCC) | ascF | beta‑glucoside specific PTS enzyme IIBC component |
| * | NC_000913 | 1,739,564 | 0 | T | G | 38.6% | 551.8 / 68.5 | 254 | T79P (ACC→CCC) | punR | DNA‑binding transcriptional activator PunR |
| * | NC_000913 | 2,189,874 | 0 | C | A | 38.1% | 65.5 / 47.2 | 42 | R346L (CGT→CTT) | yehB | putative fimbrial usher protein YehB |
| * | NC_000913 | 4,101,507 | 0 | T | G | 34.8% | 843.3 / 84.3 | 353 | intergenic (+77/‑183) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 930,061 | 0 | A | G | 34.6% | 537.0 / 181.3 | 329 | F301S (TTC→TCC) | cydD | glutathione/L‑cysteine ABC exporter subunit CydD |
| * | NC_000913 | 2,417,946 | 0 | T | G | 34.6% | 493.8 / 102.1 | 260 | V289G (GTA→GGA) | yfcC | putative transporter YfcC |
| * | NC_000913 | 1,875,838 | 0 | A | C | 34.3% | 458.8 / 159.7 | 239 | T56P (ACC→CCC) | nimT | 2‑nitroimidazole exporter |
| * | NC_000913 | 937,942 | 0 | A | C | 34.2% | 713.7 / 57.1 | 319 | T191P (ACC→CCC) | lolA | outer membrane lipoprotein carrier protein |
| * | NC_000913 | 3,835,872 | 0 | C | G | 34.0% | 615.7 / 218.4 | 297 | A20P (GCC→CCC) | yicJ | putative xyloside transporter YicJ |
| * | NC_000913 | 4,474,689 | 0 | A | G | 33.2% | 397.7 / 64.6 | 190 | E189G (GAA→GGA) | bdcR | putative transcriptional regulator BdcR |
| * | NC_000913 | 2,001,918 | 0 | A | C | 33.1% | 727.5 / 142.4 | 311 | noncoding (189/195 nt) | fliX | small RNA FliX |
| * | NC_000913 | 1,130,379 | 0 | A | C | 33.0% | 715.6 / 38.9 | 285 | V162G (GTA→GGA) | flgA | flagellar basal body P‑ring formation protein FlgA |
| * | NC_000913 | 433,634 | 0 | T | G | 32.5% | 316.0 / 84.2 | 160 | G60G (GGT→GGG) | ribD | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase/5‑amino‑6‑(5‑phosphoribosylamino)uracil reductase |
| Marginal new junction evidence (lowest skew 10 of 20 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 4542682 = | 584 (1.390) | 23 (0.060) | 23/174 | 8.7 | 4.5% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 437 (1.150) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 567 (1.350) | 20 (0.050) | 18/174 | 9.8 | 4.0% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 436 (1.140) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 3012426 | 467 (1.110) | 9 (0.030) | 7/136 | 11.9 | 2.5% | intergenic (+33/+188) | yqeA/yqeB | putative amino acid kinase YqeA/XdhC‑CoxI family protein YqeB |
| ? | NC_000913 | 3012607 = | 364 (1.220) | intergenic (+214/+7) | yqeA/yqeB | putative amino acid kinase YqeA/XdhC‑CoxI family protein YqeB | |||||
| * | ? | NC_000913 | = 374985 | 308 (0.730) | 19 (0.050) | 10/176 | 12.1 | 6.5% | intergenic (+104/‑474) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 4633096 = | 265 (0.690) | intergenic (+10/+137) | trpR/yjjX | DNA‑binding transcriptional repressor TrpR/inosine/xanthosine triphosphatase | |||||
| * | ? | NC_000913 | = 781446 | 424 (1.010) | 143 (0.430) | 7/152 | 12.5 | 35.9% | intergenic (+2/‑131) | lysZ/lysQ | tRNA‑Lys/tRNA‑Lys |
| ? | NC_000913 | 781811 = | 175 (0.530) | intergenic (+159/‑274) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | = 780631 | 473 (1.130) | 142 (0.430) | 6/152 | 12.9 | 34.1% | intergenic (+2/‑134) | lysT/valT | tRNA‑Lys/tRNA‑Val |
| ? | NC_000913 | 781811 = | 175 (0.530) | intergenic (+159/‑274) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | 3203212 = | 376 (0.890) | 61 (0.150) +A |
8/190 | 13.2 | 13.8% | intergenic (+83/+98) | cca/bacA | fused CCA tRNA nucleotidyltransferase/phosphohydrolase/undecaprenyl pyrophosphate phosphatase |
| ? | NC_000913 | 4295852 = | 396 (0.940) | intergenic (+58/+584) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO | |||||
| * | ? | NC_000913 | = 374985 | 314 (0.750) | 13 (0.030) | 7/176 | 13.2 | 3.5% | intergenic (+104/‑474) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 3150672 = | 420 (1.090) | intergenic (+126/+146) | yghA/exbD | NADP(+)‑dependent aldehyde reductase/Ton complex subunit ExbD | |||||
| * | ? | NC_000913 | = 1287084 | 351 (0.830) | 57 (0.170) | 5/152 | 13.4 | 16.5% | noncoding (153/171 nt) | rttR | small RNA RttR |
| ? | NC_000913 | 1287557 = | 299 (0.900) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 781222 | 331 (0.790) | 147 (0.430) | 5/156 | 13.5 | 39.8% | noncoding (76/76 nt) | lysY | tRNA‑Lys |
| ? | NC_000913 | 781809 = | 175 (0.510) | intergenic (+157/‑276) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||