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 |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| MC JC | 19,238 | Δ558 bp | IS1‑mediated | [nhaR] | [nhaR] |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 285,054 | C→A | T618T (ACC→ACA) | yagF → | CP4‑6 prophage; D‑xylonate dehydratase |
| RA | 527,765 | T→C | I62T (ATA→ACA) | ybbC → | PF15631 family protein YbbC |
| RA | 658,820 | G→T | intergenic (+2/‑127) | ybeM → / → tatE | deamidated glutathione amidase, N‑terminal fragment/twin arginine protein translocation system ‑ TatE protein |
| RA | 726,385 | C→A | E218* (GAA→TAA) | kdpB ← | K(+) transporting P‑type ATPase subunit KdpB |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 1,197,555 | A→G | F228S (TTC→TCC) | ymfE ← | e14 prophage; uncharacterized protein YmfE |
| RA | 1,287,614 | A→G | noncoding (9/85 nt) | tyrT ← | tRNA‑Tyr |
| RA | 1,678,604 | G→T | A60S (GCA→TCA) | ydgH → | DUF1471 domain‑containing protein YdgH |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,081,905 | G→T | Q215K (CAA→AAA) | dacD ← | D‑alanyl‑D‑alanine carboxypeptidase DacD |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,625,164 | A→T | D17V (GAT→GTT) | ppx → | exopolyphosphatase |
| RA | 2,695,699 | C→A | intergenic (‑156/‑102) | purL ← / → mltF | phosphoribosylformylglycinamide synthetase/membrane‑bound lytic murein transglycosylase F |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,932,598 | G→T | S428I (AGC→ATC) | kup → | K(+):H(+) symporter Kup |
| RA | 4,261,710 | C→A | S14R (AGC→AGA) | dusA → | tRNA‑dihydrouridine synthase A |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,367,598 | C→A | E244* (GAG→TAG) | aspA ← | aspartate ammonia‑lyase |
| RA | 4,417,219 | G→T | E90* (GAA→TAA) | yjfP → | carboxylesterase |
| RA | 4,502,068 | C→A | intergenic (+479/+35) | yjgZ → / ← insG | KpLE2 phage‑like element; uncharacterized protein YjgZ/KpLE2 phage‑like element; IS4 putative transposase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3102994 | 3104069 | 1076 | 19 [17] | [18] 19 | mutY | mutY |
| * | * | ÷ | NC_000913 | 3423787–3424231 | 3424531–3424239 | 9–745 | 20 [17] | [18] 19 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 374921 = | NA (NA) | 65 (1.250) | 25/190 | 0.8 | NA | intergenic (+40/‑538) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377531 = | NA (NA) | intergenic (+220/+4) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 374963 | NA (NA) | 34 (0.660) | 16/190 | 1.8 | 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 | 375001 = | NA (NA) | 53 (0.900) | 24/216 | 1.2 | NA | noncoding (17/36 nt) | other | REP31b |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 375082 = | NA (NA) | 56 (0.860) | 20/238 | 1.9 | NA | intergenic (+201/‑377) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377372 = | NA (NA) | noncoding (37/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 375102 = | NA (NA) | 40 (0.680) | 15/216 | 2.3 | NA | noncoding (17/36 nt) | other | REP31d |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 1207790 = | 7 (0.090) | 87 (1.300) | 55/244 | 0.1 | 95.0% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 3 (0.040) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 7 (0.090) | 51 (0.760) | 34/244 | 0.7 | 91.7% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 3 (0.040) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 67 (0.910) | 51/268 | 0.2 | 100% | intergenic (+253/‑33) | ychE/insH21 | putative inner membrane protein/IS5 transposase and trans‑activator |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+151/‑484) | insH21/oppA | IS5 transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 3363001 = | 101 (1.340) | 149 (1.990) | 64/274 | 0.1 | 74.3% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 3 (0.040) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 89 (1.180) | 50/276 | 0.3 | 96.7% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 3 (0.040) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||