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 | 84,415 | A→G | K16K (AAA→AAG) | leuO → | DNA‑binding transcriptional dual regulator LeuO |
| RA | 123,000 | T→C | intergenic (+144/‑17) | pdhR → / → aceE | DNA‑binding transcriptional dual regulator PdhR/pyruvate dehydrogenase E1 component |
| RA | 181,614 | A→G | N244S (AAC→AGC) | degP → | periplasmic serine endoprotease DegP |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 280,365 | G→A | intergenic (‑490/+20) | insA‑2 ← / ← yagB | IS1 protein InsA/orphan antitoxin YagB |
| RA | 369,972 | (G)5→6 | coding (1362/1665 nt) | mhpA → | putative 3‑(3‑hydroxyphenyl)propanoate/3‑hydroxycinnamate hydroxylase |
| RA | 496,136 | C→T | L339L (CTC→CTT) | htpG → | chaperone protein HtpG |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 527,643 | A→G | T21T (ACA→ACG) | ybbC → | PF15631 family protein YbbC |
| RA | 598,133 | A→G | T219A (ACC→GCC) | cusB → | copper/silver export system membrane fusion protein |
| RA | 615,816 | T→C | S554P (TCG→CCG) | entF → | apo‑serine activating enzyme |
| RA | 786,632 | A→G | T334A (ACC→GCC) | aroG → | 3‑deoxy‑7‑phosphoheptulonate synthase, Phe‑sensitive |
| RA | 822,571 | A→G | V390A (GTT→GCT) | clsB ← | cardiolipin synthase B |
| RA | 827,152 | A→G | V34A (GTG→GCG) | ybhS ← | putative ABC exporter membrane subunit YbhS |
| RA | 839,650 | A→G | W628R (TGG→CGG) | fiu ← | putative iron siderophore outer membrane transporter |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 892,432 | A→G | T156A (ACG→GCG) | rimK → | ribosomal protein S6 modification protein |
| RA | 915,225 | (C)5→4 | intergenic (‑368/+127) | lysO ← / ← aqpZ | L‑lysine exporter/water channel AqpZ |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,059,166 | A→G | K361K (AAA→AAG) | torC → | cytochrome c menaquinol dehydrogenase TorC |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,159,785 | A→G | S589S (AGT→AGC) | fhuE ← | ferric coprogen/ferric rhodotorulic acid outer membrane transporter |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,341,528 | A→G | Y324C (TAC→TGC) | lapB → | lipopolysaccharide assembly protein B |
| RA | 1,522,012 | A→G | F352L (TTC→CTC) | yncD ← | putative TonB‑dependent outer membrane receptor |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,634,642 | C→T | G82S (GGC→AGC) | tfaQ ← | Qin prophage; putative tail fiber assembly protein TfaQ |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,716,417 | T→C | Y269C (TAC→TGC) | tyrS ← | tyrosine‑‑tRNA ligase |
| RA | 1,723,731 | T→C | H537H (CAT→CAC) | ydhK → | putative transporter YdhK |
| RA | 1,740,447 | G→A | W179* (TGG→TGA) | ydhC → | putative transporter YdhC |
| RA | 1,762,714 | T→C | E432E (GAA→GAG) | sufB ← | Fe‑S cluster scaffold complex subunit SufB |
| RA | 1,845,334 | (T)6→5 | coding (1627/1962 nt) | topB ← | DNA topoisomerase III |
| RA | 1,873,384 | A→G | K448K (AAA→AAG) | dgcJ → | putative diguanylate cyclase DgcJ |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | 1,904,050 | C→T | R52R (CGC→CGT) | manZ → | mannose‑specific PTS enzyme IID component |
| RA | 1,938,454 | T→C | L269S (TTG→TCG) | pykA → | pyruvate kinase II |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,104,882 | (A)9→8 | coding (203/591 nt) | wbbJ ← | putative acyl transferase |
| RA | 2,109,385 | G→A | A67V (GCA→GTA) | rfbX ← | polyisoprenol‑linked O‑antigen repeat unit flippase |
| RA | 2,153,048 | A→G | D27D (GAT→GAC) | yegL ← | IPR002035 domain‑containing protein YegL |
| RA | 2,165,573 | (C)6→7 | intergenic (+52/‑95) | yegP → / → yegQ | DUF1508 domain‑containing protein YegP/putative peptidase YegQ |
| RA | 2,171,781 | T→C | intergenic (‑54/+52) | gatR ← / ← gatD | DNA‑binding transcriptional repressor GatR, N‑terminal fragment/galactitol‑1‑phosphate 5‑dehydrogenase |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,183,161 | T→C | E164G (GAA→GGA) | yegX ← | putative hydrolase |
| RA | 2,202,735 | (C)5→4 | coding (2457/3633 nt) | yehI → | DUF4132 domain‑containing protein YehI |
| RA | 2,277,320 | A→G | S341G (AGC→GGC) | yejF → | putative oligopeptide ABC transporter ATP binding subunit |
| RA | 2,277,598 | T→C | R433R (CGT→CGC) | yejF → | putative oligopeptide ABC transporter ATP binding subunit |
| RA | 2,309,798 | A→G | V203A (GTG→GCG) | ada ← | DNA‑binding transcriptional dual regulator/DNA repair protein Ada |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,456,408 | G→A | S135S (AGC→AGT) | sixA ← | phosphohistidine phosphatase |
| RA | 2,509,917 | G→A | P96P (CCG→CCA) | yfeO → | putative transport protein YfeO |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,528,811 | C→T | D456N (GAC→AAC) | ligA ← | DNA ligase |
| RA | 2,552,261 | A→G | intergenic (‑123/‑91) | ypeA ← / → amiA | putative acetyltransferase YpeA/N‑acetylmuramoyl‑L‑alanine amidase A |
| RA | 2,587,747 | C→T | G51G (GGC→GGT) | acrD → | multidrug efflux pump RND permease AcrD |
| RA | 2,602,017 | (C)7→8 | coding (200/2019 nt) | hyfB → | hydrogenase 4 component B |
| RA | 2,605,262 | C→T | A151V (GCG→GTG) | hyfD → | hydrogenase 4 component D |
| RA | 2,651,060 | G→A | R410C (CGT→TGT) | yfhM ← | alpha2‑macroglobulin |
| RA | 2,654,208 | T→C | E242E (GAA→GAG) | sseB ← | protein SseB |
| RA | 2,680,766 | A→G | C660C (TGT→TGC) | yphG ← | DUF5107 domain‑containing protein YphG |
| RA | 2,712,013 | T→C | S532P (TCC→CCC) | nadB → | L‑aspartate oxidase |
| RA | 2,734,543 | (C)8→9 | coding (492/732 nt) | pgeF ← | polyphenol oxidase YfiH |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,891,864 | G→A | P12L (CCG→CTG) | cysJ ← | sulfite reductase, flavoprotein subunit |
| RA | 2,904,086 | G→A | intergenic (+712/+661) | ygcE → / ← queE | putative sugar kinase YgcE/putative 7‑carboxy‑7‑deazaguanine synthase QueE |
| RA | 2,905,219 | (C)6→7 | coding (200/672 nt) | queE ← | putative 7‑carboxy‑7‑deazaguanine synthase QueE |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,957,507 | T→C | S460G (AGC→GGC) | ptrA ← | protease 3 |
| RA | 2,976,578 | T→C | intergenic (‑193/‑21) | omrB ← / → galR | small regulatory RNA OmrB/DNA‑binding transcriptional dual regulator GalR |
| RA | 3,035,757 | A→G | G175G (GGT→GGC) | prfB ← | peptide chain release factor RF2 |
| RA | 3,041,072 | T→C | intergenic (‑2/‑241) | sdhE ← / → ygfZ | FAD assembly factor/folate‑binding protein |
| RA | 3,045,565 | T→C | T113A (ACG→GCG) | ygfF ← | putative NAD(P)‑binding oxidoreductase with NAD(P)‑binding Rossmann‑fold domain |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,098,925 | T→C | D214G (GAT→GGT) | yggM ← | DUF1202 domain‑containing protein YggM |
| RA | 3,138,694 | G→A | intergenic (‑172/‑33) | gss ← / → yghU | fused glutathionylspermidine amidase/glutathionylspermidine synthetase/disulfide reductase/organic hydroperoxide reductase |
| RA | 3,172,594 | A→G | D22G (GAC→GGC) | mdaB → | NADPH:quinone oxidoreductase MdaB |
| RA | 3,260,051 | G→A | G20G (GGC→GGT) | tdcF ← | putative enamine/imine deaminase |
| RA | 3,316,522 | T→C | E335E (GAA→GAG) | nusA ← | transcription termination/antitermination protein NusA |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,554,315 | T→C | L411L (TTG→CTG) | malT → | DNA‑binding transcriptional activator MalT |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,565,695 | T→C | D296G (GAC→GGC) | glgP ← | glycogen phosphorylase |
| RA | 3,636,286 | (C)6→7 | coding (1125/1203 nt) | yhiN ← | putative oxidoreductase YhiN |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 3,933,167 | A→G | T618A (ACT→GCT) | kup → | K(+):H(+) symporter Kup |
| RA | 3,948,805 | (G)6→7 | coding (1165/1521 nt) | yifB ← | putative magnesium chelatase YifB |
| RA | 3,987,575 | A→G | V103A (GTT→GCT) | hemY ← | protein HemY |
| RA | 4,101,513 | (T)7→6 | intergenic (+83/‑177) | sodA → / → kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| RA | 4,103,165 | A→G | Q115R (CAG→CGG) | yiiM → | 2‑amino‑6‑N‑hydroxylaminopurine resistance protein |
| RA | 4,117,834 | A→G | V86A (GTT→GCT) | glpF ← | glycerol facilitator |
| RA | 4,138,587 | A→G | V150A (GTC→GCC) | gldA ← | L‑1,2‑propanediol dehydrogenase/glycerol dehydrogenase |
| RA | 4,178,536 | G→A | Q30Q (CAG→CAA) | rplK → | 50S ribosomal subunit protein L11 |
| RA | 4,241,331 | C→T | G308G (GGG→GGA) | xylE ← | D‑xylose:H(+) symporter |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,368,924 | A→G | L87L (TTA→TTG) | fxsA → | protein FxsA |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,565,915 | A→G | intergenic (‑65/+51) | yjiM ← / ← yjiN | putative dehydratase subunit/DUF445 domain‑containing protein YjiN |
| RA | 4,569,452 | A→G | pseudogene (455/921 nt) | rpnD → | truncated recombination‑promoting nuclease‑like protein RpnD |
| RA | 4,570,149 | C→T | intergenic (+231/+13) | rpnD → / ← yjiR | truncated recombination‑promoting nuclease‑like protein RpnD/fused putative DNA‑binding transcriptional regulator/putative aminotransferase YjiR |
| RA | 4,586,594 | (G)6→7 | coding (168/3513 nt) | hsdR ← | type I restriction enzyme EcoKI endonuclease component |
| RA | 4,624,721 | T→C | L23L (TTA→TTG) | ytjB ← | protein Smp |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423770–3424234 | 3424526–3424238 | 5–757 | 28 [23] | [24] 28 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3619350–3621083 | 3622761–3622384 | 1302–3412 | 28 [22] | [26] 29 | rhsB | rhs element protein RhsB |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 82 (0.900) | 54 (0.670) | 40/246 | 0.6 | 46.5% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 52 (0.650) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 82 (0.900) | 42 (0.520) | 31/246 | 1.2 | 40.3% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 52 (0.650) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 84 (0.950) | 54/270 | 0.3 | 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 = | 162 (1.790) | 151 (1.680) | 70/276 | 0.1 | 65.0% | 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) | 126 (1.390) | 74/278 | 0.0 | 92.0% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 11 (0.120) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | 4542682 = | 32 (0.350) | 20 (0.240) | 19/260 | 2.9 | 33.1% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 51 (0.600) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 32 (0.350) | 22 (0.260) | 20/260 | 2.8 | 35.2% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 51 (0.600) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||