mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 257,901 | G→T | intergenic (+2/+22) | crl → / ← insB9 | RNA polymerase holoenzyme assembly factor Crl/IS1 family transposase B |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 270,287 | A→C | pseudogene (10/263 nt) | insN → | IS911A regulator fragment |
| RA | 270,298 | C→T | pseudogene (21/263 nt) | insN → | IS911A regulator fragment |
| RA | 270,304 | G→A | pseudogene (27/263 nt) | insN → | IS911A regulator fragment |
| RA | 270,307 | T→C | pseudogene (30/263 nt) | insN → | IS911A regulator fragment |
| RA | 270,309 | A→G | pseudogene (32/263 nt) | insN → | IS911A regulator fragment |
| RA | 270,313 | C→T | pseudogene (36/263 nt) | insN → | IS911A regulator fragment |
| RA | 270,319 | C→A | pseudogene (42/263 nt) | insN → | IS911A regulator fragment |
| RA | 270,322 | T→C | pseudogene (45/263 nt) | insN → | IS911A regulator fragment |
| RA | 270,325 | A→G | pseudogene (48/263 nt) | insN → | IS911A regulator fragment |
| RA | 270,331 | C→T | pseudogene (54/263 nt) | insN → | IS911A regulator fragment |
| RA | 270,334 | T→G | pseudogene (57/263 nt) | insN → | IS911A regulator fragment |
| RA | 270,337 | C→T | pseudogene (60/263 nt) | insN → | IS911A regulator fragment |
| RA | 270,346 | C→T | pseudogene (69/263 nt) | insN → | IS911A regulator fragment |
| RA | 270,349 | C→A | pseudogene (72/263 nt) | insN → | IS911A regulator fragment |
| RA | 270,352 | G→T | pseudogene (75/263 nt) | insN → | IS911A regulator fragment |
| RA | 270,361 | A→C | pseudogene (84/263 nt) | insN → | IS911A regulator fragment |
| RA | 270,364 | C→G | pseudogene (87/263 nt) | insN → | IS911A regulator fragment |
| RA | 270,366 | 2 bp→AA | pseudogene (89‑90/263 nt) | insN → | IS911A regulator fragment |
| RA | 270,370 | T→C | pseudogene (93/263 nt) | insN → | IS911A regulator fragment |
| RA | 270,374 | G→A | pseudogene (97/263 nt) | insN → | IS911A regulator fragment |
| RA | 270,382 | C→G | pseudogene (105/263 nt) | insN → | IS911A regulator fragment |
| RA | 270,391 | 2 bp→CT | pseudogene (114‑115/263 nt) | insN → | IS911A regulator fragment |
| RA | 270,400 | A→G | pseudogene (123/263 nt) | insN → | IS911A regulator fragment |
| RA | 270,406 | G→A | pseudogene (129/263 nt) | insN → | IS911A regulator fragment |
| RA | 270,409 | A→G | pseudogene (132/263 nt) | insN → | IS911A regulator fragment |
| RA | 270,418 | T→G | pseudogene (141/263 nt) | insN → | IS911A regulator fragment |
| RA | 270,421 | T→C | pseudogene (144/263 nt) | insN → | IS911A regulator fragment |
| RA | 270,427 | +G | pseudogene (150/263 nt) | insN → | IS911A regulator fragment |
| RA | 270,432 | Δ1 bp | pseudogene (155/263 nt) | insN → | IS911A regulator fragment |
| RA | 270,442 | A→G | pseudogene (165/263 nt) | insN → | IS911A regulator fragment |
| RA | 270,448 | C→A | pseudogene (171/263 nt) | insN → | IS911A regulator fragment |
| RA | 270,454 | C→T | pseudogene (177/263 nt) | insN → | IS911A regulator fragment |
| RA | 270,457 | T→C | pseudogene (180/263 nt) | insN → | IS911A regulator fragment |
| RA | 270,460 | C→G | pseudogene (183/263 nt) | insN → | IS911A regulator fragment |
| RA | 270,475 | A→G | pseudogene (198/263 nt) | insN → | IS911A regulator fragment |
| RA | 270,478 | C→A | pseudogene (201/263 nt) | insN → | IS911A regulator fragment |
| RA | 270,487 | C→G | pseudogene (210/263 nt) | insN → | IS911A regulator fragment |
| RA | 270,489 | G→A | pseudogene (212/263 nt) | insN → | IS911A regulator fragment |
| RA | 270,496 | 2 bp→AA | pseudogene (219‑220/263 nt) | insN → | IS911A regulator fragment |
| RA | 270,499 | A→T | pseudogene (222/263 nt) | insN → | IS911A regulator fragment |
| RA | 270,520 | T→C | pseudogene (243/263 nt) | insN → | IS911A regulator fragment |
| RA | 284,535 | T→G | A445A (GCT→GCG) | yagF → | D‑xylonate dehydratase |
| JC JC | 572,511 | IS2 (–) +5 bp | coding (46‑50/456 nt) | ybcN → | DNA base‑flipping protein |
| RA | 635,355 | G→A | R8* (CGA→TGA) N405N (AAC→AAT) |
ybdM ← ybdN ← |
ParB‑like nuclease domain‑containing protein YbdM putative PAPS reductase/DUF3440 domain‑containing protein YbdN |
| MC JC | 678,984 | Δ8,867 bp | IS5‑mediated | [ybeT]–gltI | [ybeT], ybeU, djlC, hscC, rihA, gltL, gltK, gltJ, sroC, gltI |
| RA | 696,582 | C→T | noncoding (35/75 nt) | glnV ← | tRNA‑Gln |
| RA | 715,765 | C→T | P118P (CCC→CCT) | ybfP → | lipoprotein YbfP |
| RA | 811,531 | G→A | G384D (GGT→GAT) V4I (GTT→ATT) |
bioF → bioC → |
8‑amino‑7‑oxononanoate synthase malonyl‑acyl carrier protein methyltransferase |
| JC JC | 1,091,130 | IS2 (–) +5 bp | coding (1156‑1160/2424 nt) | pgaA ← | partially deacetylated poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine export outer membrane porin |
| RA | 1,097,494 | T→A | intergenic (+665/+71) | ycdU → / ← serX | uncharacterized protein YcdU/tRNA‑Ser |
| RA | 1,169,836 | A→G | L180P (CTG→CCG) | ldtC ← | L,D‑transpeptidase LdtC |
| RA | 1,189,980 | A→G | T156T (ACT→ACC) | phoP ← | DNA‑binding transcriptional dual regulator PhoP |
| RA | 1,301,992 | A→T | N271Y (AAT→TAT) | oppA → | oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,306,736 | T→G | S325A (TCC→GCC) | oppF → | murein tripeptide ABC transporter/oligopeptide ABC transporter ATP binding subunit OppF |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| RA | 1,358,859 | T→C | Y110C (TAT→TGT) | puuP ← | putrescine:H(+) symporter PuuP |
| RA | 1,399,493 | G→A | Q12* (CAG→TAG) | fnr ← | DNA‑binding transcriptional dual regulator FNR |
| JC JC | 1,434,586 | IS2 (+) +5 bp | intergenic (‑180/+595) | ynaM ← / ← uspF | protein YnaM/universal stress protein F |
| JC JC | 1,465,517 | IS2 (–) +5 bp | pseudogene (126‑130/2518 nt) | ydbA → | putative outer membrane protein, N‑terminal fragment |
| RA | 1,643,679 | A→T | L209Q (CTG→CAG) | ydfU ← | protein YdfU |
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| RA | 1,705,108 | G→A | G54R (GGG→AGG) | cnu → | H‑NS‑ and StpA‑binding protein |
| MC JC | 1,978,503 | Δ776 bp | insB5–insA5 | insB5, insA5 | |
| JC JC | 1,979,486 | IS5 (–) +4 bp | intergenic (‑271/‑264) | insA5 ← / → uspC | IS1 family protein InsA/universal stress protein C |
| RA | 2,040,433 | C→A | A319D (GCC→GAC) | msrP → | protein‑L‑methionine sulfoxide reductase catalytic subunit MsrP |
| RA | 2,173,363 | Δ2 bp | intergenic (‑490/+918) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| JC JC | 2,176,322 | IS1 (–) +9 bp | intergenic (‑1/+20) | gatZ ← / ← gatY | putative tagatose‑1,6‑bisphosphate aldolase 2 chaperone/tagatose‑1,6‑bisphosphate aldolase 2 |
| JC JC | 2,319,848 | IS2 (+) +5 bp | coding (25‑29/2850 nt) | rcsC ← | histidine kinase RcsC |
| MC JC | 2,558,699 | Δ6,790 bp | intZ–[eutA] | intZ, yffL, yffM, yffN, yffO, yffP, yffQ, yffR, yffS, [eutA] | |
| RA | 2,867,455 | G→A | Q33* (CAG→TAG) | rpoS ← | RNA polymerase sigma factor RpoS |
| RA | 3,388,041 | T→G | T50P (ACG→CCG) | aaeB ← | aromatic carboxylic acid efflux pump subunit AaeB |
| JC JC | 3,533,058 | IS2 (–) +5 bp | coding (241‑245/1623 nt) | pck → | phosphoenolpyruvate carboxykinase (ATP) |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| RA | 3,707,947 | C→A | intergenic (‑242/+669) | dppA ← / ← proK | dipeptide ABC transporter periplasmic binding protein/tRNA‑Pro |
| JC JC | 3,890,222 | IS5 (–) +4 bp | intergenic (+77/‑11) | tnaA → / → tnaB | tryptophanase/tryptophan:H(+) symporter TnaB |
| RA | 4,132,697 | G→A | E28K (GAG→AAG) | metF → | 5,10‑methylenetetrahydrofolate reductase |
| RA | 4,223,638 | T→C | intergenic (‑10/‑190) | iclR ← / → metH | DNA‑binding transcriptional repressor IclR/cobalamin‑dependent methionine synthase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,510,238 | T→G | intergenic (+445/+452) | insO → / ← fecE | IS911B regulator fragment/ferric citrate ABC transporter ATP binding subunit |
| RA | 4,566,642 | G→A | S202L (TCG→TTG) | yjiN ← | DUF445 domain‑containing protein YjiN |
| RA | 4,569,394 | T→C | intergenic (‑667/+768) | ytiE ← / ← yjiR | protein YtiE/fused putative DNA‑binding transcriptional regulator/putative aminotransferase YjiR |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 260173 | 270275 | 10103 | 126 [0] | [39] 40 | proB–perR | proB,proA,thrW,ykfI,yafW,ykfH,ykfG,yafX,ykfF,ykfB,yafY,yafZ,ykfA,perR |
| * | * | ÷ | NC_000913 | 270541–271294 | 274932–273956 | 2663–4392 | 41 [38] | [36] 41 | insI1–[insH1] | insI1,insN,eyeA,ykfC,[insH1] |
| * | * | ÷ | NC_000913 | 3423806–3424234 | 3424482–3424239 | 6–677 | 43 [39] | [39] 40 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 260172 | 0 (0.000) | 126 (1.190) | 92/598 | 0.0 | 100% | intergenic (‑72/‑216) | phoE/proB | outer membrane porin PhoE/glutamate 5‑kinase |
| ? | NC_000913 | 273955 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 1207790 = | 38 (0.360) | 69 (0.690) | 46/566 | 1.0 | 65.4% | coding (290/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | 1209619 = | 37 (0.370) | intergenic (‑500/‑66) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1207805 | 37 (0.350) | 74 (0.740) | 54/566 | 0.6 | 67.3% | coding (305/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | = 1209602 | 37 (0.370) | intergenic (‑483/‑83) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||