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 22 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 3,206,435 | 0 | C | T | 42.9% | 28.4 / 28.3 | 35 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,604,344 | 0 | C | T | 41.7% | 40.0 / 36.0 | 48 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 4,296,060 | 0 | C | T | 37.5% | 106.1 / 89.3 | 88 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 29,496 | 0 | T | A | 36.0% | 75.7 / 35.4 | 50 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 1,068,173 | 0 | T | G | 33.8% | 104.3 / 27.5 | 68 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| * | NC_000913 | 650,809 | 0 | T | G | 33.8% | 110.8 / 37.5 | 80 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 753,125 | 0 | T | A | 32.9% | 141.7 / 45.4 | 79 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 4,568,504 | 0 | T | G | 32.6% | 152.9 / 18.5 | 99 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 1,825,061 | 0 | G | A | 29.7% | 69.5 / 13.2 | 37 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 3,206,444 | 0 | T | A | 29.3% | 72.8 / 12.0 | 41 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 2,326,450 | 0 | T | G | 28.8% | 73.3 / 34.9 | 52 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 4,111,747 | 0 | G | T | 28.3% | 139.6 / 23.4 | 53 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 3,556,205 | 0 | A | C | 27.6% | 46.8 / 10.2 | 29 | S215R (AGT→AGG) | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 4,429,984 | 0 | T | G | 26.7% | 106.1 / 20.9 | 60 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 2,001,918 | 0 | A | C | 25.9% | 156.3 / 24.2 | 81 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 1,491,098 | 0 | A | C | 25.3% | 140.7 / 12.8 | 75 | Y66S (TAC→TCC) | cybB | cytochrome b561 |
| * | NC_000913 | 753,114 | 0 | G | T | 24.4% | 218.8 / 17.1 | 82 | intergenic (‑319/+71) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 4,032,731 | 0 | T | G | 23.7% | 151.8 / 17.9 | 76 | G80G (GGT→GGG) | yigZ | IMPACT family member YigZ |
| * | NC_000913 | 445,558 | 0 | A | C | 22.4% | 92.8 / 20.7 | 49 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 175,694 | 0 | T | G | 21.1% | 151.8 / 10.4 | 71 | G196G (GGT→GGG) | clcA | chloride:H(+) antiporter ClcA |
| 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 | 78 (0.910) | 14 (0.180) | 14/258 | 3.7 | 15.9% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 75 (0.940) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 2405937 | 96 (1.120) | 15 (0.180) | 13/274 | 4.2 | 13.8% | coding (705/939 nt) | lrhA | DNA‑binding transcriptional dual regulator LrhA |
| ? | NC_000913 | 2405949 = | 92 (1.080) | coding (693/939 nt) | lrhA | DNA‑binding transcriptional dual regulator LrhA | |||||
| * | ? | NC_000913 | = 374963 | NA (NA) | 7 (0.120) | 6/190 | 4.8 | NA | noncoding (33/34 nt) | other | REP31a |
| ? | NC_000913 | = 377487 | NA (NA) | intergenic (+176/+48) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 4542682 = | 88 (1.030) | 10 (0.130) | 9/258 | 5.1 | 11.2% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 76 (0.950) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 375124 = | NA (NA) | 5 (0.080) | 4/192 | 5.8 | NA | intergenic (+243/‑335) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377530 = | NA (NA) | intergenic (+219/+5) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 374921 = | NA (NA) | 6 (0.100) | 4/190 | 5.8 | NA | intergenic (+40/‑538) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377531 = | NA (NA) | intergenic (+220/+4) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 8 (0.100) | 5/260 | 6.7 | NA | intergenic (+41/‑537) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377329 = | NA (NA) | intergenic (+18/+206) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 4512063 | 84 (0.980) | 4 (0.050) | 4/256 | 7.1 | 4.8% | coding (352/957 nt) | fecD | ferric citrate ABC transporter membrane subunit FecD |
| ? | NC_000913 | = 4512138 | 80 (1.010) | coding (277/957 nt) | fecD | ferric citrate ABC transporter membrane subunit FecD | |||||
| * | ? | NC_000913 | = 375266 | NA (NA) | 3 (0.040) | 3/238 | 7.4 | NA | noncoding (33/34 nt) | other | REP31g |
| ? | NC_000913 | = 377487 | NA (NA) | intergenic (+176/+48) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 375145 | NA (NA) | 4 (0.050) +A |
4/274 | 7.4 | NA | noncoding (13/34 nt) | other | REP31e |
| ? | NC_000913 | = 377506 | NA (NA) | noncoding (17/34 nt) | other | REP32d | |||||