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 | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
RA | 354,503 | G→A | A600T (GCG→ACG) | prpE → | propionyl‑CoA synthetase |
RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
RA | 1,196,220 | C→T | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase |
RA | 1,196,232 | C→T | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase |
RA | 1,196,245 | T→C | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
RA | 1,196,247 | A→G | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
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 | 2,003,448 | A→C | R53R (CGT→CGG) | fliC ← | flagellar filament structural protein |
JC JC | 2,169,898 | IS1 (+) +9 bp | pseudogene (262‑270/475 nt) | gatR ← | DNA‑binding transcriptional repressor GatR, N‑terminal fragment |
RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
RA | 2,617,797 | G→C | A74P (GCT→CCT) | yfgD → | putative oxidoreductase YfgD |
RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
JC | 3,447,581 | +GGC | coding (187/315 nt) | rplX ← | 50S ribosomal subunit protein L24 |
RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
RA | 3,647,083 | G→A | G262D (GGT→GAT) | gor → | glutathione reductase (NADPH) |
RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
RA | 3,892,014 | G→T | G134C (GGT→TGT) | mdtL → | efflux pump MdtL |
MC JC | 4,082,677 | Δ204 bp | [fdoH]–[fdoG] | [fdoH], [fdoG] | |
RA | 4,274,902 | C→T | G47D (GGC→GAC) | yjcB ← | uncharacterized protein YjcB |
RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
RA | 4,623,281 | Δ2 bp | coding (836‑837/1017 nt) | lplA ← | lipoate‑‑protein ligase A |
Unassigned missing coverage evidence | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|
seq id | start | end | size | ←reads | reads→ | gene | description | |||
* | * | ÷ | NC_000913 | 1196260 | 1211431 | 15172 | 25 [24] | [22] 25 | [icd]–[icdC] | [icd],ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,oweE,ymfN,aaaE,ymfR,beeE,jayE,ymfQ,ycfK,tfaP,tfaE,stfE,pinE,mcrA,[icdC] |
* | * | ÷ | NC_000913 | 3423770–3424234 | 3424530–3424238 | 5–761 | 27 [24] | [24] 25 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
Unassigned new junction evidence | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | NC_000913 | = 1299498 | 0 (0.000) | 76 (0.770) | 47/268 | 0.6 | 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 | 2481751 = | 63 (0.620) | 49 (0.490) | 28/270 | 1.8 | 36.1% | coding (426/1539 nt) | emrY | tripartite efflux pump membrane subunit EmrY |
? | NC_000913 | = 2481901 | 112 (1.130) | coding (276/1539 nt) | emrY | tripartite efflux pump membrane subunit EmrY | |||||
* | ? | NC_000913 | 3363001 = | 177 (1.750) | 171 (1.700) | 73/274 | 0.1 | 65.4% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
? | NC_000913 | 3766087 = | 5 (0.050) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
* | ? | NC_000913 | = 3653230 | NA (NA) | 111 (1.100) | 58/276 | 0.3 | 95.7% | noncoding (1/1195 nt) | IS5 | repeat region |
? | NC_000913 | = 3766089 | 5 (0.050) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA |