mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.27.0b revision f32c2f7f32bc
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 1889 shown) | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | A | a | var freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 417,533 | 0 | T | T | G | 44.7% | 210.4 / 64.8 | 199 | V131G (GTG→GGG) | phoB | response regulator in two‑component regulatory system with PhoR |
| * | NC_000913 | 2,228,275 | 0 | T | T | C | 44.1% | 319.6 / 59.8 | 237 | pseudogene (335/1287 nt) | mdtQ | pseudogene; putative channel/filament proteins |
| * | NC_000913 | 743,657 | 0 | T | T | G | 41.2% | 260.5 / 25.9 | 215 | V22G (GTG→GGG) | ybgJ | putative allophanate hydrolase, subunit 1 |
| * | NC_000913 | 433,649 | 0 | T | T | G | 41.2% | 266.5 / 82.8 | 323 | G65G (GGT→GGG) | ribD | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase |
| * | NC_000913 | 283,940 | 0 | A | A | G | 39.6% | 155.5 / 14.2 | 111 | E247G (GAG→GGG) | yagF | CP4‑6 prophage; dehydratase family protein |
| * | NC_000913 | 4,622,250 | 0 | A | A | G | 38.6% | 501.9 / 127.3 | 277 | E161G (GAG→GGG) | yjjJ | putative protein kinase |
| * | NC_000913 | 4,604,344 | 0 | C | C | T | 38.4% | 616.9 / 241.1 | 400 | S62F (TCT→TTT) | bglJ | bgl operon transcriptional activator |
| * | NC_000913 | 811,721 | 0 | T | T | G | 38.3% | 618.7 / 33.9 | 327 | V67G (GTG→GGG) | bioC | malonyl‑ACP O‑methyltransferase, SAM‑dependent |
| * | NC_000913 | 3,206,446 | 0 | C | C | A | 38.3% | 594.7 / 168.5 | 362 | intergenic (‑190/‑17) | ttdR/ttdA | transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit |
| * | NC_000913 | 2,228,272 | 0 | A | A | C | 38.1% | 433.6 / 48.1 | 246 | pseudogene (338/1287 nt) | mdtQ | pseudogene; putative channel/filament proteins |
| * | NC_000913 | 288,382 | 0 | A | A | C | 37.8% | 278.7 / 39.6 | 173 | T532P (ACC→CCC) | yagH | CP4‑6 prophage; putative xylosidase/arabinosidase |
| * | NC_000913 | 4,457,105 | 0 | A | A | G | 37.5% | 608.1 / 139.2 | 342 | I441V (ATC→GTC) | mpl | UDP‑N‑acetylmuramate:L‑alanyl‑gamma‑D‑glutamyl‑ meso‑diaminopimelate ligase |
| * | NC_000913 | 4,101,507 | 0 | T | T | G | 37.5% | 981.6 / 65.7 | 465 | intergenic (+77/‑183) | sodA/kdgT | superoxide dismutase, Mn/2‑keto‑3‑deoxy‑D‑gluconate transporter |
| * | NC_000913 | 3,401,459 | 0 | T | T | C | 37.5% | 586.5 / 109.0 | 315 | D625G (GAT→GGT) | csrD | targeting factor for csrBC sRNA degradation |
| * | NC_000913 | 2,151,689 | 0 | G | G | T | 37.4% | 180.8 / 80.3 | 212 | intergenic (+43/+22) | yegJ/yegK | uncharacterized protein/ser/thr phosphatase‑related protein |
| * | NC_000913 | 3,133,302 | 0 | T | T | G | 37.3% | 757.8 / 111.5 | 376 | H219P (CAC→CCC) | yghS | putative ATP‑binding protein |
| * | NC_000913 | 2,326,450 | 0 | T | T | G | 37.1% | 680.6 / 127.2 | 345 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 273,676 | 0 | T | T | G | 37.0% | 987.8 / 77.1 | 450 | pseudogene (830/1108 nt) | ykfC | CP4‑6 prophage; conserved protein;Phage or Prophage Related |
| * | NC_000913 | 2,151,686 | 0 | G | G | T | 37.0% | 196.1 / 88.6 | 212 | intergenic (+40/+25) | yegJ/yegK | uncharacterized protein/ser/thr phosphatase‑related protein |
| * | NC_000913 | 2,074,044 | 0 | T | T | C | 36.9% | 239.5 / 18.7 | 123 | S836P (TCC→CCC) | flu | CP4‑44 prophage; antigen 43 (Ag43) phase‑variable biofilm formation autotransporter |
| Marginal new junction evidence (lowest skew 10 of 55 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 4542682 = | 500 (1.210) | 29 (0.070) | 25/308 | 9.8 | 6.0% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | 4542996 = | 440 (1.130) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | 1097039 = | 219 (0.530) | 64 (0.160) +C |
24/324 | 10.6 | 24.0% | intergenic (+210/+526) | ycdU/serX | putative inner membrane protein/tRNA‑Ser |
| ? | NC_000913 | = 1097580 | 188 (0.460) | noncoding (73/88 nt) | serX | tRNA‑Ser | |||||
| * | ? | NC_000913 | = 382590 | NA (NA) | 31 (0.080) | 24/326 | 10.7 | 5.9% | noncoding (1331/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 564107 = | 491 (1.190) | coding (374/633 nt) | sfmZ | response regulator family protein | |||||
| * | ? | NC_000913 | 381260 = | NA (NA) | 27 (0.070) | 18/324 | 12.6 | 5.1% | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 564111 | 502 (1.220) | coding (370/633 nt) | sfmZ | response regulator family protein | |||||
| * | ? | NC_000913 | 3652036 = | NA (NA) | 100 (0.240) | 17/326 | 13.0 | 16.3% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3890078 | 513 (1.240) | coding (1349/1416 nt) | tnaA | tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent | |||||
| * | ? | NC_000913 | 1097029 = | 228 (0.550) | 48 (0.120) +C |
17/324 | 13.0 | 19.1% | intergenic (+200/+536) | ycdU/serX | putative inner membrane protein/tRNA‑Ser |
| ? | NC_000913 | = 1097570 | 180 (0.440) | noncoding (83/88 nt) | serX | tRNA‑Ser | |||||
| * | ? | NC_000913 | = 2290113 | NA (NA) | 17 (0.040) | 16/326 | 13.4 | 3.2% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 3890075 = | 510 (1.230) | coding (1346/1416 nt) | tnaA | tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent | |||||
| * | ? | NC_000913 | = 4542690 | 541 (1.310) | 13 (0.030) | 11/308 | 15.1 | 2.7% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | = 4542986 | 440 (1.130) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | = 3815858 | 424 (1.030) | 10 (0.030) | 9/306 | 16.1 | 2.8% | pseudogene (24/48 nt) | rph | ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
| ? | NC_000913 | 3815941 = | 290 (0.750) | pseudogene (609/669 nt) | rph | ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH | |||||
| * | ? | NC_000913 | 2139570 = | 291 (0.700) | 7 (0.020) | 7/304 | 17.2 | 2.6% | intergenic (+85/+189) | yegH/asmA | inner membrane protein/suppressor of OmpF assembly mutants; putative outer membrane protein assembly factor; inner membrane‑anchored periplasmic protein |
| ? | NC_000913 | 2139603 = | 243 (0.630) | intergenic (+118/+156) | yegH/asmA | inner membrane protein/suppressor of OmpF assembly mutants; putative outer membrane protein assembly factor; inner membrane‑anchored periplasmic protein | |||||