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 |
| RA | 248,194 | G→T | intergenic (+60/+164) | rayT → / ← lfhA | REP‑associated tyrosine transposase/flagellar system protein, promoterless fragment |
| RA | 248,197 | T→A | intergenic (+63/+161) | rayT → / ← lfhA | REP‑associated tyrosine transposase/flagellar system protein, promoterless fragment |
| RA | 248,205 | C→A | intergenic (+71/+153) | rayT → / ← lfhA | REP‑associated tyrosine transposase/flagellar system protein, promoterless fragment |
| RA | 248,219 | T→C | intergenic (+85/+139) | rayT → / ← lfhA | REP‑associated tyrosine transposase/flagellar system protein, promoterless fragment |
| RA | 248,221 | T→C | intergenic (+87/+137) | rayT → / ← lfhA | REP‑associated tyrosine transposase/flagellar system protein, promoterless fragment |
| RA | 248,263 | G→A | intergenic (+129/+95) | rayT → / ← lfhA | REP‑associated tyrosine transposase/flagellar system protein, promoterless fragment |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 286,882 | G→T | E32* (GAG→TAG) | yagH → | CP4‑6 prophage; putative xylosidase/arabinosidase |
| JC JC | 584,565 | IS1 (–) +9 bp | intergenic (+135/+107) | appY → / ← ompT | DNA‑binding transcriptional activator AppY/outer membrane protease VII (outer membrane protein 3b) |
| RA | 607,090 | G→T | G98G (GGC→GGA) | ybdK ← | carboxylate‑amine ligase |
| 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 |
| JC JC | 1,646,627 | IS5 (–) +4 bp | coding (223‑226/333 nt) | flxA → | Qin prophage; protein FlxA |
| 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 | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,657,434 | G→A | S501F (TCT→TTT) | hscA ← | iron‑sulfur cluster biosynthesis chaperone HscA |
| RA | 2,911,176 | Δ1 bp | coding (164/249 nt) | mazE ← | antitoxin of the MazF‑MazE toxin‑antitoxin system MazE |
| RA | 2,995,683 | T→C | pseudogene (338/707 nt) | ygeN ← | putative type III secretion system protein |
| 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 | 3,760,398 | C→A | A284A (GCG→GCT) | selA ← | selenocysteine synthase |
| RA | 3,805,227 | C→A | E242* (GAA→TAA) | waaP ← | lipopolysaccharide core heptose (I) kinase |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,907,051 | C→A | M176I (ATG→ATT) | phoU ← | negative regulator of the pho regulon |
| RA | 4,261,710 | C→A | S14R (AGC→AGA) | dusA → | tRNA‑dihydrouridine synthase A |
| RA | 4,292,086 | G→T | R192L (CGC→CTC) | nrfE → | putative cytochrome c‑type biogenesis protein NrfE |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196245 | 1211437 | 15193 | 19 [15] | [15] 19 | [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 | 3102983 | 3104081 | 1099 | 17 [16] | [16] 20 | mutY | mutY |
| * | * | ÷ | NC_000913 | 3423759–3424233 | 3424536–3424239 | 7–778 | 17 [16] | [16] 18 | [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) | 71 (1.290) | 51/268 | 0.1 | 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 = | 74 (1.310) | 83 (1.480) | 56/274 | 0.0 | 68.5% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 3 (0.050) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 50 (0.890) | 36/276 | 0.4 | 92.6% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 4 (0.070) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||