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 | 40.7% | 55.7 / 39.9 | 59 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 3,206,444 | 0 | T | A | 34.1% | 63.7 / 23.8 | 44 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 3,206,435 | 0 | C | T | 34.0% | 57.0 / 31.5 | 47 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 2,001,918 | 0 | A | C | 33.3% | 73.6 / 20.1 | 45 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,111,747 | 0 | G | T | 33.3% | 68.7 / 24.8 | 36 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 1,550,663 | 0 | A | C | 29.3% | 76.5 / 11.2 | 41 | N68T (AAC→ACC) | fdnH | formate dehydrogenase N subunit beta |
| * | NC_000913 | 445,558 | 0 | A | C | 29.0% | 53.6 / 13.7 | 32 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 4,287,719 | 0 | T | A | 26.2% | 168.9 / 33.9 | 84 | intergenic (‑348/‑45) | acs/nrfA | acetyl‑CoA synthetase (AMP‑forming)/cytochrome c552 nitrite reductase |
| * | NC_000913 | 3,006,012 | 0 | C | T | 25.0% | 105.1 / 13.9 | 52 | intergenic (‑226/‑250) | ygeV/ygeW | putative sigma(54)‑dependent transcriptional regulator YgeV/putative carbamoyltransferase YgeW |
| * | NC_000913 | 3,740,909 | 0 | T | G | 25.0% | 141.7 / 11.4 | 68 | V402G (GTG→GGG) | avtA | valine‑‑pyruvate aminotransferase |
| * | NC_000913 | 2,326,450 | 0 | T | G | 24.3% | 80.0 / 10.4 | 37 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 650,809 | 0 | T | G | 23.5% | 111.4 / 10.0 | 52 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 4,568,504 | 0 | T | G | 23.4% | 249.9 / 10.5 | 115 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 2,483,268 | 0 | T | A | 21.9% | 158.2 / 13.6 | 64 | L24F (TTA→TTT) | emrK | tripartite efflux pump membrane fusion protein EmrK |
| * | NC_000913 | 4,568,512 | 0 | C | A | 21.3% | 248.2 / 30.2 | 89 | R3L (CGT→CTT) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 4,101,514 | 0 | G | T | 20.8% | 133.0 / 11.9 | 48 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 4,429,984 | 0 | T | G | 20.0% | 157.7 / 16.6 | 65 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| Marginal new junction evidence (lowest skew 10 of 26 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 375102 = | NA (NA) | 25 (0.390) | 12/216 | 3.2 | NA | noncoding (17/36 nt) | other | REP31d |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | = 1207805 | 61 (0.740) | 14 (0.190) | 13/244 | 3.5 | 19.5% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 62 (0.860) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 375064 | NA (NA) | 17 (0.300) | 9/192 | 3.6 | NA | noncoding (33/34 nt) | other | REP31c |
| ? | NC_000913 | = 377487 | NA (NA) | intergenic (+176/+48) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 4542690 | 64 (0.780) | 15 (0.200) | 13/258 | 3.7 | 19.3% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 66 (0.860) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 16 (0.270) | 9/202 | 3.8 | 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 | = 4373285 | NA (NA) | 9 (0.130) | 9/226 | 4.2 | NA | noncoding (12/34 nt) | other | REP328b |
| ? | NC_000913 | = 4374507 | NA (NA) | noncoding (9/34 nt) | other | REP329a | |||||
| * | ? | NC_000913 | 1207790 = | 65 (0.790) | 12 (0.170) | 10/244 | 4.2 | 16.4% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 65 (0.900) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 555833 | 87 (1.060) | 9 (0.120) | 8/244 | 4.8 | 10.4% | coding (1223/1386 nt) | cysS | cysteine‑‑tRNA ligase |
| ? | NC_000913 | = 556784 | 78 (1.080) | coding (90/213 nt) | ybcJ | putative RNA‑binding protein YbcJ | |||||
| * | ? | NC_000913 | 2514273 = | NA (NA) | 5 (0.080) | 5/224 | 5.6 | 7.6% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 2515618 = | 61 (0.920) | intergenic (+175/+25) | insL‑3/pdeA | putative IS186/IS421 transposase/putative c‑di‑GMP phosphodiesterase PdeA | |||||
| * | ? | NC_000913 | 4542682 = | 73 (0.890) | 6 (0.080) | 6/258 | 5.8 | 8.2% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 66 (0.860) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||