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 21 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,604,344 | 0 | C | T | 40.8% | 74.9 / 53.1 | 71 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 1,825,061 | 0 | G | A | 37.5% | 38.0 / 15.5 | 32 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 4,568,504 | 0 | T | G | 33.8% | 132.4 / 14.9 | 80 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 3,206,435 | 0 | C | T | 33.3% | 36.0 / 14.4 | 27 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 753,125 | 0 | T | A | 30.6% | 65.6 / 14.7 | 36 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 4,429,984 | 0 | T | G | 29.7% | 62.8 / 12.1 | 37 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 3,556,207 | 0 | T | C | 27.8% | 62.6 / 11.6 | 36 | S215G (AGT→GGT) | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 29,496 | 0 | T | A | 27.5% | 88.4 / 15.9 | 40 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 2,001,918 | 0 | A | C | 27.1% | 89.5 / 15.1 | 48 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,568,512 | 0 | C | A | 27.0% | 172.1 / 27.7 | 63 | R3L (CGT→CTT) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 2,326,450 | 0 | T | G | 26.5% | 118.9 / 37.4 | 68 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 445,558 | 0 | A | C | 25.6% | 72.4 / 13.8 | 39 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 1,491,098 | 0 | A | C | 25.6% | 147.9 / 17.4 | 78 | Y66S (TAC→TCC) | cybB | cytochrome b561 |
| * | NC_000913 | 729,659 | 0 | T | G | 25.4% | 137.2 / 12.3 | 68 | V26G (GTA→GGA) | rhsC | rhs element protein RhsC |
| * | NC_000913 | 372,640 | 0 | T | G | 25.0% | 109.3 / 15.1 | 56 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 4,296,060 | 0 | C | T | 24.7% | 182.3 / 51.8 | 85 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 4,287,719 | 0 | T | A | 23.8% | 152.2 / 27.2 | 63 | intergenic (‑348/‑45) | acs/nrfA | acetyl‑CoA synthetase (AMP‑forming)/cytochrome c552 nitrite reductase |
| * | NC_000913 | 1,550,663 | 0 | A | C | 22.4% | 104.3 / 10.1 | 49 | N68T (AAC→ACC) | fdnH | formate dehydrogenase N subunit beta |
| * | NC_000913 | 1,068,173 | 0 | T | G | 21.9% | 180.9 / 18.4 | 82 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| * | NC_000913 | 646,747 | 0 | T | G | 21.8% | 118.9 / 14.8 | 55 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| 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 | 70 (0.830) | 11 (0.140) | 8/258 | 5.3 | 12.1% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 95 (1.210) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 76 (0.900) | 10 (0.130) | 8/258 | 5.3 | 10.8% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 95 (1.210) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 3411703 | 87 (1.040) | 4 (0.050) | 4/270 | 7.2 | 4.4% | coding (51/885 nt) | yhdJ | DNA adenine methyltransferase |
| ? | NC_000913 | 3411707 = | 87 (1.060) | coding (55/885 nt) | yhdJ | DNA adenine methyltransferase | |||||
| * | ? | NC_000913 | = 3743489 | 73 (0.870) | 3 (0.040) | 3/270 | 7.7 | 4.0% | coding (757/999 nt) | yiaK | 2,3‑diketo‑L‑gulonate reductase |
| ? | NC_000913 | 3743493 = | 72 (0.880) | coding (761/999 nt) | yiaK | 2,3‑diketo‑L‑gulonate reductase | |||||
| * | ? | NC_000913 | = 3146969 | 74 (0.880) | 3 (0.040) | 3/268 | 7.7 | 4.0% | pseudogene (723/836 nt) | yghX | putative hydrolase fragment |
| ? | NC_000913 | 3146974 = | 73 (0.890) | pseudogene (718/836 nt) | yghX | putative hydrolase fragment | |||||
| * | ? | NC_000913 | = 4299785 | 74 (0.880) | 3 (0.040) | 3/272 | 7.8 | 3.9% | coding (1246/1467 nt) | mdtP | putative multidrug efflux pump outer membrane channel |
| ? | NC_000913 | 4299790 = | 73 (0.880) | coding (1241/1467 nt) | mdtP | putative multidrug efflux pump outer membrane channel | |||||
| * | ? | NC_000913 | = 2270006 | 72 (0.860) | 3 (0.040) | 3/272 | 7.8 | 4.1% | coding (28/567 nt) | mepS | peptidoglycan DD‑endopeptidase/peptidoglycan LD‑carboxypeptidase |
| ? | NC_000913 | 2270011 = | 71 (0.860) | coding (33/567 nt) | mepS | peptidoglycan DD‑endopeptidase/peptidoglycan LD‑carboxypeptidase | |||||