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 29 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 | 44.7% | 120.8 / 113.1 | 141 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 3,556,205 | 0 | A | C | 32.8% | 121.1 / 19.4 | 64 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 753,125 | 0 | T | A | 32.4% | 117.3 / 36.3 | 68 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 3,556,207 | 0 | T | C | 31.8% | 102.6 / 21.4 | 63 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 2,001,918 | 0 | A | C | 31.2% | 140.2 / 37.2 | 77 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,568,504 | 0 | T | G | 30.7% | 251.9 / 21.5 | 140 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 445,558 | 0 | A | C | 29.2% | 112.9 / 38.5 | 65 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 372,640 | 0 | T | G | 27.2% | 209.6 / 31.3 | 103 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 4,296,060 | 0 | C | T | 26.9% | 226.0 / 88.2 | 130 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 3,206,435 | 0 | C | T | 26.9% | 115.9 / 31.2 | 67 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 2,628,625 | 0 | A | C | 26.7% | 129.3 / 16.3 | 60 | V105G (GTC→GGC) | pdeF | cyclic di‑GMP phosphodiesterase PdeF |
| * | NC_000913 | 1,550,663 | 0 | A | C | 26.2% | 169.6 / 28.0 | 80 | N68T (AAC→ACC) | fdnH | formate dehydrogenase N subunit beta |
| * | NC_000913 | 4,223,593 | 0 | T | G | 25.6% | 287.2 / 25.4 | 125 | K12N (AAA→AAC) | iclR | DNA‑binding transcriptional repressor IclR |
| * | NC_000913 | 753,114 | 0 | G | T | 25.4% | 180.1 / 16.4 | 71 | intergenic (‑319/+71) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 4,628,649 | 0 | A | C | 25.0% | 212.3 / 24.6 | 92 | intergenic (+102/+206) | nadR/ettA | DNA‑binding transcriptional repressor/NMN adenylyltransferase NadR/energy‑dependent translational throttle protein EttA |
| * | NC_000913 | 4,111,747 | 0 | G | T | 24.6% | 178.6 / 27.4 | 65 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 888,014 | 0 | T | G | 24.6% | 129.1 / 11.3 | 57 | noncoding (44/81 nt) | rybB | small regulatory RNA RybB |
| * | NC_000913 | 3,206,444 | 0 | T | A | 24.2% | 129.0 / 14.9 | 62 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 2,326,450 | 0 | T | G | 24.1% | 248.8 / 49.7 | 113 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 4,429,984 | 0 | T | G | 23.6% | 285.2 / 45.0 | 123 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| Marginal new junction evidence (lowest skew 10 of 37 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 375203 = | NA (NA) | 22 (0.190) | 15/216 | 4.3 | NA | noncoding (17/36 nt) | other | REP31f |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | = 375219 | NA (NA) | 19 (0.160) | 14/216 | 4.6 | NA | noncoding (1/36 nt) | other | REP31f |
| ? | NC_000913 | = 377333 | NA (NA) | intergenic (+22/+202) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 4542682 = | 111 (0.730) | 21 (0.150) | 17/258 | 4.7 | 15.1% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 132 (0.930) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 374963 | NA (NA) | 18 (0.170) | 10/190 | 5.1 | 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 | 375102 = | NA (NA) | 28 (0.240) | 11/216 | 5.3 | NA | noncoding (17/36 nt) | other | REP31d |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | = 4542690 | 107 (0.700) | 14 (0.100) | 13/258 | 5.6 | 10.8% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 130 (0.910) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 375118 | NA (NA) | 13 (0.110) | 9/216 | 6.0 | NA | noncoding (1/36 nt) | other | REP31d |
| ? | NC_000913 | = 377333 | NA (NA) | intergenic (+22/+202) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 375320 | NA (NA) | 11 (0.090) | 8/232 | 6.6 | NA | noncoding (1/36 nt) | other | REP31h |
| ? | NC_000913 | = 377333 | NA (NA) | intergenic (+22/+202) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 375001 = | NA (NA) | 14 (0.120) | 7/216 | 6.7 | NA | noncoding (17/36 nt) | other | REP31b |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | = 375059 | NA (NA) | 8 (0.050) +T |
7/274 | 7.8 | NA | noncoding (28/34 nt) | other | REP31c |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||