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 | 1,894,666 | 0 | T | C | 74.4% | 248.1 / 83.0 | 133 | E22E (GAA→GAG) | yoaH | UFP0181 family protein YoaH |
| * | NC_000913 | 4,604,344 | 0 | C | T | 38.1% | 80.7 / 33.8 | 64 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 3,556,207 | 0 | T | C | 34.5% | 76.8 / 25.6 | 55 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 3,556,205 | 0 | A | C | 31.5% | 91.0 / 17.3 | 54 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 4,296,060 | 0 | C | T | 31.3% | 155.5 / 80.4 | 99 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 3,943,488 | 0 | T | G | 29.3% | 59.4 / 15.3 | 41 | noncoding (54/76 nt) | gltU | tRNA‑Glu |
| * | NC_000913 | 753,125 | 0 | T | A | 27.7% | 134.3 / 23.7 | 65 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 2,001,918 | 0 | A | C | 27.5% | 96.9 / 16.4 | 51 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,111,747 | 0 | G | T | 26.1% | 123.4 / 19.3 | 46 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 4,111,752 | 0 | T | C | 25.9% | 111.4 / 12.3 | 58 | K155E (AAA→GAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 4,568,504 | 0 | T | G | 25.9% | 217.7 / 17.4 | 118 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 445,558 | 0 | A | C | 25.0% | 77.7 / 12.1 | 41 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 650,809 | 0 | T | G | 23.8% | 163.3 / 20.5 | 80 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 29,496 | 0 | T | A | 23.4% | 156.0 / 18.6 | 64 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 3,206,435 | 0 | C | T | 22.6% | 110.7 / 17.6 | 53 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 1,775,467 | 0 | A | C | 21.3% | 126.8 / 10.2 | 61 | intergenic (+23/‑120) | aroD/ydiF | 3‑dehydroquinate dehydratase/putative acetate‑CoA transferase |
| * | NC_000913 | 3,401,459 | 0 | T | C | 21.1% | 201.1 / 19.1 | 95 | D625G (GAT→GGT) | csrD | regulator of CsrB and CsrC decay |
| * | NC_000913 | 376,401 | 0 | T | G | 20.7% | 193.5 / 12.4 | 87 | L315V (TTG→GTG) | mhpT | 3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| * | NC_000913 | 1,068,173 | 0 | T | G | 20.6% | 232.1 / 16.9 | 98 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| * | NC_000913 | 2,326,450 | 0 | T | G | 20.6% | 155.1 / 21.4 | 68 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| 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 | 88 (0.890) | 20 (0.220) | 19/260 | 3.1 | 19.8% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 80 (0.860) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 97 (0.980) | 12 (0.130) | 10/260 | 5.2 | 12.3% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 81 (0.880) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 1979489 | 118 (1.190) | 5 (0.050) | 5/278 | 7.4 | 4.1% | intergenic (‑274/‑264) | insA‑5/uspC | IS1 protein InsA/universal stress protein C |
| ? | NC_000913 | = 2290113 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 1390175 = | 83 (0.840) | 4 (0.040) | 4/262 | 7.6 | 4.5% | coding (424/729 nt) | mpaA | murein tripeptide amidase A |
| ? | NC_000913 | 1390253 = | 91 (0.980) | coding (346/729 nt) | mpaA | murein tripeptide amidase A | |||||
| * | ? | NC_000913 | 315401 = | NA (NA) | 3 (0.030) | 3/252 | 8.0 | NA | noncoding (173/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | 315627 = | NA (NA) | noncoding (399/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 4534603 | 91 (0.950) | 6 (0.060) +GATGG |
3/258 | 8.1 | 6.1% | pseudogene (73/246 nt) | yjhZ | KpLE2 phage‑like element; putative acetyltransferase YjhZ |
| ? | NC_000913 | 4534604 = | 96 (0.970) | pseudogene (72/246 nt) | yjhZ | KpLE2 phage‑like element; putative acetyltransferase YjhZ | |||||
| * | ? | NC_000913 | = 3117052 | 144 (1.450) | 3 (0.030) | 3/274 | 8.4 | 2.0% | coding (2061/4563 nt) | yghJ | putative lipoprotein YghJ |
| ? | NC_000913 | 3117056 = | 145 (1.490) | coding (2057/4563 nt) | yghJ | putative lipoprotein YghJ | |||||
| * | ? | NC_000913 | = 1123665 | 69 (0.700) | 5 (0.050) | 3/274 | 8.4 | 5.0% | coding (390/648 nt) | grxB | reduced glutaredoxin 2 |
| ? | NC_000913 | 2723583 = | 124 (1.270) | coding (857/1356 nt) | pssA | phosphatidylserine synthase | |||||