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 23 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 2,001,918 | 0 | A | C | 37.8% | 106.2 / 44.5 | 83 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,604,344 | 0 | C | T | 36.7% | 139.6 / 65.8 | 109 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 445,558 | 0 | A | C | 31.9% | 64.1 / 24.5 | 47 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 501,575 | 0 | A | C | 30.8% | 119.0 / 24.2 | 66 | V555G (GTG→GGG) | ybaL | putative transporter YbaL |
| * | NC_000913 | 372,640 | 0 | T | G | 29.6% | 126.2 / 24.8 | 72 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 4,111,747 | 0 | G | T | 29.2% | 166.1 / 34.5 | 65 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 501,572 | 0 | A | C | 27.3% | 137.7 / 12.9 | 66 | V556G (GTG→GGG) | ybaL | putative transporter YbaL |
| * | NC_000913 | 4,568,504 | 0 | T | G | 26.1% | 312.9 / 15.1 | 154 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 2,326,450 | 0 | T | G | 25.7% | 197.2 / 50.9 | 101 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 3,240,985 | 0 | T | G | 24.8% | 209.2 / 23.1 | 101 | S348A (TCT→GCT) | sstT | serine/threonine:Na(+) symporter |
| * | NC_000913 | 501,564 | 0 | A | C | 24.7% | 153.3 / 36.8 | 77 | *559E (TAA→GAA) | ybaL | putative transporter YbaL |
| * | NC_000913 | 1,825,061 | 0 | G | A | 24.5% | 111.2 / 15.7 | 53 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 646,747 | 0 | T | G | 24.1% | 119.6 / 21.2 | 58 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 753,125 | 0 | T | A | 23.6% | 177.4 / 19.8 | 72 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 4,429,984 | 0 | T | G | 21.9% | 222.4 / 22.4 | 96 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 2,667,126 | 0 | A | C | 21.6% | 186.6 / 10.8 | 88 | Y241D (TAT→GAT) | hcaT | putative 3‑phenylpropionate transporter |
| * | NC_000913 | 1,335,691 | 0 | T | G | 21.6% | 245.3 / 17.1 | 116 | intergenic (+24/‑140) | ymiC/acnA | protein YmiC/aconitate hydratase 1 |
| * | NC_000913 | 3,275,611 | 0 | A | C | 21.5% | 187.6 / 10.8 | 79 | E110D (GAA→GAC) | garD | galactarate dehydratase |
| * | NC_000913 | 4,098,155 | 0 | A | C | 21.3% | 332.1 / 16.2 | 151 | L140F (TTA→TTC) | rhaS | DNA‑binding transcriptional activator RhaS |
| * | NC_000913 | 3,926,366 | 0 | A | C | 20.8% | 336.4 / 37.6 | 149 | G30G (GGT→GGG) | mioC | flavoprotein MioC |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4542690 | 105 (0.780) | 14 (0.110) | 9/260 | 6.9 | 11.4% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 119 (0.940) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 122 (0.900) | 8 (0.060) | 8/260 | 7.2 | 6.4% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 120 (0.950) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 153209 | 165 (1.220) | 3 (0.020) | 3/264 | 9.8 | 2.0% | coding (2218/2598 nt) | htrE | putative fimbrial usher protein HtrE |
| ? | NC_000913 | = 153237 | 133 (1.040) | coding (2190/2598 nt) | htrE | putative fimbrial usher protein HtrE | |||||
| * | ? | NC_000913 | = 3416154 | 195 (1.440) | 3 (0.020) | 3/272 | 9.9 | 1.6% | coding (1122/3105 nt) | acrF | multidrug efflux pump RND permease AcrF |
| ? | NC_000913 | 3416158 = | 177 (1.340) | coding (1126/3105 nt) | acrF | multidrug efflux pump RND permease AcrF | |||||
| * | ? | NC_000913 | = 3495187 | 131 (0.970) | 3 (0.020) | 3/276 | 10.0 | 2.3% | coding (1177/2544 nt) | nirB | nitrite reductase catalytic subunit NirB |
| ? | NC_000913 | 3495191 = | 130 (0.970) | coding (1181/2544 nt) | nirB | nitrite reductase catalytic subunit NirB | |||||
| * | ? | NC_000913 | = 1042817 | 116 (0.860) | 3 (0.020) | 3/274 | 10.0 | 2.5% | coding (1394/2181 nt) | etk | protein‑tyrosine kinase Etk |
| ? | NC_000913 | 1042824 = | 115 (0.860) | coding (1387/2181 nt) | etk | protein‑tyrosine kinase Etk | |||||