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 | 4,568,504 | 0 | T | G | 33.8% | 142.4 / 13.9 | 81 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 372,640 | 0 | T | G | 32.6% | 69.4 / 11.8 | 43 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 2,326,450 | 0 | T | G | 32.4% | 54.1 / 20.5 | 37 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 3,206,435 | 0 | C | T | 32.3% | 38.5 / 17.8 | 31 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,604,344 | 0 | C | T | 29.1% | 146.5 / 33.7 | 87 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 4,111,747 | 0 | G | T | 28.3% | 124.1 / 20.6 | 46 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 753,125 | 0 | T | A | 27.9% | 86.6 / 16.5 | 43 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 1,491,098 | 0 | A | C | 25.4% | 123.8 / 14.3 | 63 | Y66S (TAC→TCC) | cybB | cytochrome b561 |
| * | NC_000913 | 445,558 | 0 | A | C | 24.1% | 52.3 / 10.6 | 29 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 888,014 | 0 | T | G | 23.3% | 90.4 / 10.2 | 43 | noncoding (44/81 nt) | rybB | small regulatory RNA RybB |
| * | NC_000913 | 1,068,173 | 0 | T | G | 22.4% | 128.4 / 12.8 | 58 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| * | NC_000913 | 4,296,060 | 0 | C | T | 21.6% | 182.8 / 44.8 | 88 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 4,287,719 | 0 | T | A | 21.3% | 117.6 / 11.9 | 48 | intergenic (‑348/‑45) | acs/nrfA | acetyl‑CoA synthetase (AMP‑forming)/cytochrome c552 nitrite reductase |
| * | NC_000913 | 3,531,440 | 0 | A | C | 21.2% | 182.0 / 14.1 | 80 | Y334D (TAT→GAT) | yhgE | putative transport protein YhgE |
| * | NC_000913 | 3,206,444 | 0 | T | A | 20.9% | 96.6 / 11.0 | 43 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| Marginal new junction evidence (lowest skew 10 of 11 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4542690 | 66 (0.860) | 14 (0.200) | 14/258 | 3.6 | 15.0% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 97 (1.350) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 71 (0.930) | 5 (0.070) | 5/258 | 6.6 | 5.8% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 97 (1.350) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 1468807 | NA (NA) | 21 (0.290) +GGGCGC |
3/250 | 7.6 | NA | noncoding (434/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 1468808 = | NA (NA) | noncoding (433/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 1142150 = | 67 (0.870) | 3 (0.040) | 3/250 | 7.6 | 5.5% | coding (2218/3186 nt) | rne | ribonuclease E |
| ? | NC_000913 | 1142653 = | 43 (0.620) | coding (1715/3186 nt) | rne | ribonuclease E | |||||
| * | ? | NC_000913 | = 462691 | 71 (0.930) | 3 (0.040) | 3/258 | 7.7 | 4.8% | coding (777/1872 nt) | ppiD | periplasmic folding chaperone |
| ? | NC_000913 | = 462899 | 52 (0.730) | coding (985/1872 nt) | ppiD | periplasmic folding chaperone | |||||
| * | ? | NC_000913 | 4440559 = | 109 (1.420) | 3 (0.040) | 3/262 | 7.8 | 2.7% | coding (657/1344 nt) | ytfL | putative inner membrane protein |
| ? | NC_000913 | 4440675 = | 111 (1.520) | coding (541/1344 nt) | ytfL | putative inner membrane protein | |||||
| * | ? | NC_000913 | = 4022825 | 76 (0.990) | 3 (0.040) | 3/264 | 7.8 | 3.6% | coding (90/777 nt) | tatC | twin arginine protein translocation system ‑ TatC protein |
| ? | NC_000913 | = 4022858 | 88 (1.200) | coding (123/777 nt) | tatC | twin arginine protein translocation system ‑ TatC protein | |||||
| * | ? | NC_000913 | = 2134182 | 59 (0.780) | 3 (0.040) +GCT |
3/266 | 7.9 | 4.9% | coding (1471/2163 nt) | wzc | protein‑tyrosine kinase Wzc |
| ? | NC_000913 | 2134183 = | 59 (0.770) | coding (1470/2163 nt) | wzc | protein‑tyrosine kinase Wzc | |||||
| * | ? | NC_000913 | 2997259 = | NA (NA) | 3 (0.040) | 3/274 | 8.0 | NA | noncoding (433/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 3186523 = | NA (NA) | noncoding (428/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 1088768 = | 76 (0.990) | 3 (0.040) | 3/274 | 8.0 | 3.4% | coding (1090/2019 nt) | pgaB | poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine N‑deacetylase and beta‑1,6 glycoside hydrolase |
| ? | NC_000913 | = 1088937 | 97 (1.270) | coding (921/2019 nt) | pgaB | poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine N‑deacetylase and beta‑1,6 glycoside hydrolase | |||||