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 | 652,063 | A→G | intergenic (‑207/‑172) | citC ← / → dpiB | citrate lyase synthetase/sensory histidine kinase DpiB |
RA | 745,356 | A→C | E64D (GAA→GAC) | pxpA → | 5‑oxoprolinase component A |
RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
RA | 1,020,961 | A→G | intergenic (‑42/‑177) | sulA ← / → sxy | cell division inhibitor SulA/transcriptional coactivator for CRP |
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 |
RA | 1,212,088 | (C)8→7 | intergenic (‑85/+172) | iraM ← / ← ymgK | anti‑adaptor protein IraM, inhibitor of sigma(S) proteolysis/protein YmgK |
RA | 1,453,709 | G→A | intergenic (‑67/‑218) | paaZ ← / → paaA | oxepin‑CoA hydrolase/3‑oxo‑5,6‑dehydrosuberyl‑CoA semialdehyde dehydrogenase/phenylacetyl‑CoA 1,2‑epoxidase, monooxygenase subunit |
JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
RA | 1,904,926 | Δ1 bp | coding (126/459 nt) | yobD → | conserved inner membrane protein YobD |
MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
JC JC | 2,168,543 | IS2 (–) +5 bp | intergenic (‑237/‑165) | yegR ← / → yegS | uncharacterized protein YegR/lipid kinase |
RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
RA | 2,947,456 | (C)5→6 | noncoding (70/77 nt) | metZ → | tRNA‑Met |
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 | 3,949,786 | C→A | A62S (GCG→TCG) | yifB ← | putative magnesium chelatase YifB |
RA | 4,025,837 | C→G | P284A (CCG→GCG) | ubiD → | 3‑octaprenyl‑4‑hydroxybenzoate decarboxylase |
RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
RA | 4,325,822 | G→A | intergenic (‑81/+577) | yjdN ← / ← yjdM | conserved protein YjdN/conserved protein YjdM |
RA | 4,325,847 | 2 bp→CA | intergenic (‑106/+551) | yjdN ← / ← yjdM | conserved protein YjdN/conserved protein YjdM |
RA | 4,392,446 | Δ1 bp | intergenic (+11/‑26) | glyV → / → glyX | tRNA‑Gly/tRNA‑Gly |
RA | 4,392,453 | C→T | intergenic (+18/‑19) | glyV → / → glyX | tRNA‑Gly/tRNA‑Gly |
RA | 4,392,456 | A→G | intergenic (+21/‑16) | glyV → / → glyX | tRNA‑Gly/tRNA‑Gly |
Unassigned missing coverage evidence | ||||||||||
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seq id | start | end | size | ←reads | reads→ | gene | description | |||
* | * | ÷ | NC_000913 | 1196270 | 1211433 | 15164 | 12 [10] | [10] 11 | [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 | 3424525–3424239 | 6–756 | 11 [9] | [10] 20 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
Unassigned new junction evidence | |||||||||||
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seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | NC_000913 | = 1299498 | 0 (0.000) | 38 (0.750) | 27/266 | 0.7 | 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 = | 76 (1.450) | 79 (1.520) | 49/272 | 0.1 | 67.4% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
? | NC_000913 | 3766087 = | 1 (0.020) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
* | ? | NC_000913 | = 3653230 | NA (NA) | 65 (1.240) | 44/274 | 0.1 | 97.0% | noncoding (1/1195 nt) | IS5 | repeat region |
? | NC_000913 | = 3766089 | 2 (0.040) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||
* | ? | NC_000913 | = 4542690 | 51 (0.970) | 14 (0.290) | 11/256 | 2.4 | 24.2% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
? | NC_000913 | = 4542986 | 40 (0.820) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |