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 | 39.0% | 88.4 / 55.5 | 82 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 3,206,435 | 0 | C | T | 37.0% | 47.4 / 31.2 | 46 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 650,809 | 0 | T | G | 35.3% | 83.5 / 20.8 | 51 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 3,556,207 | 0 | T | C | 32.6% | 65.8 / 14.7 | 43 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 445,558 | 0 | A | C | 31.1% | 77.3 / 24.2 | 45 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 3,556,205 | 0 | A | C | 30.9% | 78.4 / 10.9 | 42 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 4,296,060 | 0 | C | T | 30.5% | 168.7 / 83.3 | 105 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 2,326,450 | 0 | T | G | 29.7% | 115.8 / 37.7 | 64 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 29,496 | 0 | T | A | 29.6% | 90.6 / 28.2 | 54 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 1,550,663 | 0 | A | C | 29.2% | 90.9 / 17.8 | 48 | N68T (AAC→ACC) | fdnH | formate dehydrogenase N subunit beta |
| * | NC_000913 | 4,429,984 | 0 | T | G | 28.9% | 166.4 / 37.2 | 83 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 4,568,504 | 0 | T | G | 27.9% | 227.8 / 15.4 | 112 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 4,111,747 | 0 | G | T | 27.9% | 106.6 / 22.9 | 44 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 3,401,459 | 0 | T | C | 26.2% | 115.2 / 19.3 | 65 | D625G (GAT→GGT) | csrD | regulator of CsrB and CsrC decay |
| * | NC_000913 | 753,125 | 0 | T | A | 25.0% | 109.4 / 13.7 | 48 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 4,628,649 | 0 | A | C | 24.6% | 154.6 / 14.0 | 65 | intergenic (+102/+206) | nadR/ettA | DNA‑binding transcriptional repressor/NMN adenylyltransferase NadR/energy‑dependent translational throttle protein EttA |
| * | NC_000913 | 2,001,918 | 0 | A | C | 24.3% | 79.8 / 11.4 | 37 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 3,926,366 | 0 | A | C | 21.8% | 241.2 / 21.9 | 101 | G30G (GGT→GGG) | mioC | flavoprotein MioC |
| * | NC_000913 | 1,068,173 | 0 | T | G | 21.6% | 177.9 / 18.7 | 74 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| * | NC_000913 | 1,315,936 | 0 | T | A | 21.2% | 199.9 / 17.1 | 80 | K34* (AAA→TAA) | yciG | protein YciG |
| Marginal new junction evidence (lowest skew 10 of 41 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 375102 = | NA (NA) | 41 (0.550) | 15/216 | 3.0 | NA | noncoding (17/36 nt) | other | REP31d |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | = 1207805 | 86 (0.900) | 16 (0.190) | 16/244 | 3.3 | 16.5% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 86 (1.010) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 375160 | NA (NA) | 33 (0.350) +T |
14/274 | 4.2 | NA | noncoding (28/34 nt) | other | REP31e |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 375023 = | NA (NA) | 10 (0.150) | 8/192 | 4.3 | NA | intergenic (+142/‑436) | 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 | 375001 = | NA (NA) | 23 (0.310) | 9/216 | 4.5 | NA | noncoding (17/36 nt) | other | REP31b |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 4542682 = | 83 (0.860) | 12 (0.130) | 11/258 | 4.7 | 11.8% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 102 (1.140) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 375059 | NA (NA) | 16 (0.170) +T |
11/274 | 4.9 | NA | noncoding (28/34 nt) | other | REP31c |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | = 4542690 | 70 (0.730) | 9 (0.100) | 9/258 | 5.2 | 9.7% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 102 (1.140) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 377350 | NA (NA) | 15 (0.160) +ACG |
7/270 | 6.1 | NA | noncoding (15/37 nt) | other | REP32a |
| ? | NC_000913 | 508649 = | NA (NA) | noncoding (19/36 nt) | other | REP48b | |||||
| * | ? | NC_000913 | = 4373285 | NA (NA) | 6 (0.080) | 5/226 | 6.2 | NA | noncoding (12/34 nt) | other | REP328b |
| ? | NC_000913 | = 4374507 | NA (NA) | noncoding (9/34 nt) | other | REP329a | |||||