mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 | 85,648 | G→A | A7T (GCC→ACC) | ilvI → | acetolactate synthase/acetohydroxybutanoate synthase, catalytic subunit |
| RA | 94,844 | A→G | L65L (CTA→CTG) | murF → | D‑alanyl‑D‑alanine‑adding enzyme |
| RA | 110,388 | C→T | P704S (CCG→TCG) | secA → | protein translocation ATPase |
| RA | 116,614 | T→C | G162G (GGA→GGG) | hofB ← | T2SSE family protein |
| RA | 166,980 | A→G | T751A (ACG→GCG) | mrcB → | peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcB |
| RA | 196,336 | A→G | L220L (TTA→TTG) | cdsA → | CDP‑diglyceride synthetase |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 273,256 | A→G | E137G (GAG→GGG) | ykfC → | CP4‑6 prophage; PF00078 domain‑containing protein YkfC |
| RA | 280,366 | C→A | intergenic (‑491/+19) | insA‑2 ← / ← yagB | IS1 protein InsA/orphan antitoxin YagB |
| RA | 305,196 | G→A | R4* (CGA→TGA) A541V (GCG→GTG) |
ecpE ← ecpD ← |
putative fimbrial chaperone EcpE fimbrial adhesin EcpD |
| RA | 380,022 | (G)10→9 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 417,887 | A→G | intergenic (+56/‑2) | phoB → / → phoR | DNA‑binding transcriptional dual regulator PhoB/sensory histidine kinase PhoR |
| RA | 513,573 | T→C | V333A (GTG→GCG) | ybaT → | putative transporter YbaT |
| RA | 786,280 | (G)5→6 | coding (648/1053 nt) | aroG → | 3‑deoxy‑7‑phosphoheptulonate synthase, Phe‑sensitive |
| RA | 801,050 | T→C | S98P (TCT→CCT) | ybhH → | putative isomerase YbhH |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 1,007,086 | C→A | R172L (CGC→CTC) | ycbX ← | 6‑N‑hydroxylaminopurine resistance protein |
| RA | 1,161,855 | A→G | intergenic (‑304/‑30) | fhuE ← / → hinT | ferric coprogen/ferric rhodotorulic acid outer membrane transporter/purine nucleoside phosphoramidase |
| RA | 1,188,233 | T→C | Y3C (TAC→TGC) | roxA ← | ribosomal protein‑arginine oxygenase |
| 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 | 1,224,687 | T→C | E225E (GAA→GAG) | minD ← | Z‑ring positioning protein MinD |
| RA | 1,227,171 | A→G | L101P (CTC→CCC) | pliG ← | inhibitor of g‑type lysozyme |
| RA | 1,316,153 | A→G | intergenic (‑118/+263) | yciG ← / ← trpA | protein YciG/tryptophan synthase subunit alpha |
| RA | 1,594,132 | (C)8→7 | pseudogene (3955/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,594,256 | (C)8→9 | pseudogene (3831/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,678,604 | G→T | A60S (GCA→TCA) | ydgH → | DUF1471 domain‑containing protein YdgH |
| RA | 1,730,372 | (T)5→4 | coding (1286/4617 nt) | lhr → | putative ATP‑dependent helicase Lhr |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | 1,934,809 | T→C | intergenic (‑205/+30) | edd ← / ← zwf | phosphogluconate dehydratase/NADP(+)‑dependent glucose‑6‑phosphate dehydrogenase |
| RA | 1,967,611 | (C)5→4 | coding (891/1050 nt) | cheB ← | protein‑glutamate methylesterase/protein glutamine deamidase |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,141,427 | A→G | S62S (AGT→AGC) | asmA ← | putative assembly protein AsmA |
| RA | 2,163,830 | C→T | L319L (CTG→TTG) | baeS → | sensory histidine kinase BaeS |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,339,161 | T→G | D87A (GAC→GCC) | gyrA ← | DNA gyrase subunit A |
| RA | 2,349,578 | G→T | intergenic (‑106/‑109) | inaA ← / → yfaH | putative lipopolysaccharide kinase InaA/putative uncharacterized protein YfaH |
| RA | 2,358,767 | T→C | T27A (ACG→GCG) | yfaU ← | 2‑keto‑3‑deoxy‑L‑rhamnonate aldolase |
| RA | 2,385,869 | (A)7→8 | coding (10/972 nt) | yfbL → | putative peptidase YfbL |
| RA | 2,488,664 | T→C | T169A (ACA→GCA) | yfdE ← | acetyl‑CoA:oxalate CoA‑transferase |
| RA | 2,583,969 | (C)5→4 | coding (1557/1980 nt) | aegA ← | putative oxidoreductase Fe‑S subunit AegA |
| RA | 2,690,530 | A→G | V190A (GTA→GCA) | glrK ← | sensory histidine kinase GlrK |
| RA | 2,765,794 | (C)7→6 | intergenic (‑18/‑124) | yfjM ← / → rnlA | CP4‑57 prophage; protein YfjM/CP4‑57 prophage; RNase LS, toxin of the RnlAB toxin‑antitoxin system |
| RA | 2,781,909 | +C | coding (818/4581 nt) | ypjA ← | adhesin‑like autotransporter YpjA |
| RA | 2,904,529 | G→A | intergenic (+1155/+218) | ygcE → / ← queE | putative sugar kinase YgcE/putative 7‑carboxy‑7‑deazaguanine synthase QueE |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,412,153 | A→G | P167P (CCA→CCG) | yhdJ → | DNA adenine methyltransferase |
| RA | 3,470,718 | C→A | E204D (GAG→GAT) | tufA ← | translation elongation factor Tu 1 |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,660,720 | G→A | A103T (GCA→ACA) | mdtF → | multidrug efflux pump RND permease MdtF |
| RA | 3,741,977 | A→G | L186L (TTA→CTA) | yiaJ ← | DNA‑binding transcriptional repressor YiaJ |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,836,193 | G→T | intergenic (‑264/‑29) | yicJ ← / → selC | putative xyloside transporter YicJ/tRNA‑Sec |
| RA | 3,982,684 | (C)8→9 | noncoding (79/87 nt) | leuT → | tRNA‑Leu |
| RA | 3,996,611 | C→A | H109N (CAT→AAT) | xerC → | site‑specific tyrosine recombinase |
| RA | 4,000,272 | T→C | intergenic (+127/+20) | uvrD → / ← yigE | ssDNA translocase and dsDNA helicase ‑ DNA helicase II/DUF2233 domain‑containing protein YigE |
| RA | 4,083,975 | C→A | S616S (TCG→TCT) | fdoG ← | formate dehydrogenase O subunit alpha |
| RA | 4,147,552 | A→G | F256L (TTT→CTT) | yijO ← | putative DNA‑binding transcriptional regulator YijO |
| RA | 4,201,514 | T→C | S59G (AGC→GGC) | zraP ← | zinc responsive, periplasmic protein with chaperone activity |
| RA | 4,261,710 | C→A | S14R (AGC→AGA) | dusA → | tRNA‑dihydrouridine synthase A |
| RA | 4,262,000 | A→G | N111S (AAT→AGT) | 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 | 4,397,590 | G→T | G60V (GGC→GTC) | mutL → | DNA mismatch repair protein MutL |
| RA | 4,606,094 | (G)8→10 | noncoding (72/87 nt) | leuV ← | tRNA‑Leu |
| RA | 4,631,539 | G→T | Q269H (CAG→CAT) | slt → | soluble lytic murein transglycosylase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196275 | 1211435 | 15161 | 30 [24] | [25] 26 | [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 | 3102942 | 3104085 | 1144 | 26 [25] | [24] 26 | mutY | mutY |
| * | * | ÷ | NC_000913 | 3423758–3424233 | 3424536–3424239 | 7–779 | 26 [24] | [25] 26 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3619350–3621083 | 3622715–3622397 | 1315–3366 | 31 [24] | [24] 30 | rhsB | rhs element protein RhsB |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 160 (1.510) | 76/268 | 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 = | 195 (1.790) | 195 (1.800) | 81/274 | 0.1 | 66.6% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 2 (0.020) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 137 (1.260) | 73/276 | 0.1 | 95.1% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 7 (0.060) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||