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 30 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 | 40.3% | 79.4 / 44.7 | 67 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 29,496 | 0 | T | A | 33.3% | 119.4 / 32.8 | 63 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 372,640 | 0 | T | G | 33.3% | 97.4 / 25.7 | 63 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 4,568,504 | 0 | T | G | 32.4% | 184.1 / 19.3 | 106 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 445,558 | 0 | A | C | 29.8% | 75.0 / 26.7 | 47 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 501,572 | 0 | A | C | 29.3% | 77.7 / 10.8 | 41 | V556G (GTG→GGG) | ybaL | putative transporter YbaL |
| * | NC_000913 | 501,575 | 0 | A | C | 29.3% | 74.7 / 13.8 | 41 | V555G (GTG→GGG) | ybaL | putative transporter YbaL |
| * | NC_000913 | 3,240,985 | 0 | T | G | 28.8% | 92.4 / 16.3 | 52 | S348A (TCT→GCT) | sstT | serine/threonine:Na(+) symporter |
| * | NC_000913 | 802,118 | 0 | A | C | 28.1% | 113.9 / 14.7 | 57 | T78P (ACC→CCC) | ybhI | putative tricarboxylate transporter |
| * | NC_000913 | 650,809 | 0 | T | G | 27.7% | 121.6 / 13.9 | 65 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 2,001,918 | 0 | A | C | 26.6% | 133.0 / 15.5 | 64 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 888,014 | 0 | T | G | 26.3% | 146.5 / 19.1 | 76 | noncoding (44/81 nt) | rybB | small regulatory RNA RybB |
| * | NC_000913 | 4,296,060 | 0 | C | T | 26.3% | 151.4 / 48.6 | 76 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 3,206,435 | 0 | C | T | 25.7% | 68.1 / 12.4 | 35 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 3,556,205 | 0 | A | C | 25.6% | 87.6 / 12.3 | 43 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 1,825,061 | 0 | G | A | 24.5% | 107.7 / 14.1 | 49 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 3,404,218 | 0 | T | G | 23.9% | 150.4 / 14.5 | 67 | G245G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 2,326,450 | 0 | T | G | 23.5% | 102.8 / 21.4 | 51 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 3,556,207 | 0 | T | C | 23.3% | 86.7 / 10.9 | 43 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 753,125 | 0 | T | A | 23.1% | 194.0 / 28.6 | 78 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate 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 | 4542682 = | 103 (1.190) | 14 (0.170) | 14/258 | 4.1 | 12.7% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 97 (1.190) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 103 (1.190) | 14 (0.170) | 13/258 | 4.4 | 12.7% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 96 (1.180) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 2290113 | NA (NA) | 13 (0.150) | 5/276 | 7.6 | 12.5% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 2406443 | 91 (1.050) | coding (199/939 nt) | lrhA | DNA‑binding transcriptional dual regulator LrhA | |||||
| * | ? | NC_000913 | 374945 = | NA (NA) | 10 (0.120) +T |
5/274 | 7.6 | NA | noncoding (15/34 nt) | other | REP31a |
| ? | NC_000913 | 377408 = | NA (NA) | noncoding (15/34 nt) | other | REP32b | |||||
| * | ? | NC_000913 | 2518092 = | 97 (1.120) | 3 (0.040) | 3/240 | 8.0 | 3.9% | noncoding (25/76 nt) | alaX | tRNA‑Ala |
| ? | NC_000913 | 2521076 = | 63 (0.830) | noncoding (26/76 nt) | valX | tRNA‑Val | |||||
| * | ? | NC_000913 | = 1979632 | 111 (1.280) | 4 (0.050) | 4/268 | 8.0 | 3.5% | intergenic (‑417/‑121) | insA‑5/uspC | IS1 protein InsA/universal stress protein C |
| ? | NC_000913 | 1979637 = | 111 (1.320) | intergenic (‑422/‑116) | insA‑5/uspC | IS1 protein InsA/universal stress protein C | |||||
| * | ? | NC_000913 | = 375199 | NA (NA) | 4 (0.050) +A |
4/274 | 8.1 | NA | noncoding (21/36 nt) | other | REP31f |
| ? | NC_000913 | = 377353 | NA (NA) | noncoding (18/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | = 375098 | NA (NA) | 6 (0.070) +A |
4/274 | 8.1 | NA | noncoding (21/36 nt) | other | REP31d |
| ? | NC_000913 | = 377353 | NA (NA) | noncoding (18/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 3402429 = | 98 (1.130) | 3 (0.040) | 3/252 | 8.3 | 3.2% | coding (904/1941 nt) | csrD | regulator of CsrB and CsrC decay |
| ? | NC_000913 | 3402750 = | 90 (1.130) | coding (583/1941 nt) | csrD | regulator of CsrB and CsrC decay | |||||
| * | ? | NC_000913 | = 1221511 | 117 (1.350) | 3 (0.040) | 3/270 | 8.6 | 2.6% | pseudogene (1911/2648 nt) | ycgH | putative transporter component, N‑terminal fragment |
| ? | NC_000913 | 1221515 = | 111 (1.310) | pseudogene (1915/2648 nt) | ycgH | putative transporter component, N‑terminal fragment | |||||