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 | 59,287 | T→C | intergenic (+8/+400) | yabQ → / ← rluA | protein YabQ/23S rRNA pseudouridine(746) and tRNA pseudouridine(32) synthase |
| RA | 124,351 | T→C | G445G (GGT→GGC) | aceE → | pyruvate dehydrogenase E1 component |
| RA | 189,644 | A→G | intergenic (‑138/‑68) | map ← / → tff | methionine aminopeptidase/putative small RNA T44 |
| RA | 196,371 | T→C | V232A (GTG→GCG) | cdsA → | CDP‑diglyceride synthetase |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 294,733 | (T)5→4 | coding (67/855 nt) | yagM ← | CP4‑6 prophage; protein YagM |
| RA | 336,297 | A→G | T125A (ACC→GCC) | yahE → | DUF2877 domain‑containing protein YahE |
| RA | 348,325 | +G | coding (119/1587 nt) | prpR ← | DNA‑binding transcriptional dual regulator PrpR |
| RA | 380,022 | (G)10→11 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 399,161 | A→G | V58A (GTC→GCC) | yaiY ← | inner membrane protein |
| RA | 412,490 | C→T | intergenic (‑9/+117) | araJ ← / ← sbcC | putative transport protein AraJ/ATP dependent, structure specific DNA nuclease ‑ SbcC subunit |
| RA | 433,595 | T→C | G47G (GGT→GGC) | ribD → | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase/5‑amino‑6‑(5‑phosphoribosylamino)uracil reductase |
| RA | 468,864 | A→G | intergenic (+23/‑7) | decR → / → mdlA | DNA‑binding transcriptional activator DecR/ABC transporter family protein MdlA |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 543,355 | C→T | G231D (GGC→GAC) | allE ← | (S)‑ureidoglycine aminohydrolase |
| RA | 672,468 | C→T | L772L (CTG→CTA) | leuS ← | leucine‑‑tRNA ligase |
| RA | 685,011 | A→G | V82A (GTA→GCA) | gltL ← | glutamate/aspartate ABC transporter ATP binding subunit |
| RA | 695,193 | A→G | V31V (GTA→GTG) | ubiF → | 2‑octaprenyl‑3‑methyl‑6‑methoxy‑1,4‑benzoquinol hydroxylase |
| RA | 721,768 | T→C | T883A (ACT→GCT) | kdpD ← | sensory histidine kinase KdpD |
| RA | 734,833 | A→C | pseudogene (614/1434 nt) | ybfO → | conserved protein, rhs‑like YbfO |
| RA | 734,845 | A→G | pseudogene (626/1434 nt) | ybfO → | conserved protein, rhs‑like YbfO |
| RA | 751,395 | A→G | L259L (TTA→CTA) | ybgQ ← | putative fimbrial usher protein YbgQ |
| RA | 752,266 | A→G | V177A (GTA→GCA) | ybgD ← | putative fimbrial protein YbgD |
| RA | 766,784 | C→T | A267A (GCC→GCT) | mngA → | 2‑O‑alpha‑mannosyl‑D‑glycerate specific PTS enzyme II |
| RA | 784,507 | A→G | V106A (GTC→GCC) | zitB ← | Zn(2(+))/Cd(2(+))/Ni(2(+))/Cu(2(+)) exporter |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 923,371 | T→C | S36S (AGT→AGC) | clpA → | ATP‑dependent Clp protease ATP‑binding subunit ClpA |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 964,139 | A→G | intergenic (+27/‑181) | ihfB → / → ycaI | integration host factor subunit beta/conserved inner membrane protein YcaI |
| RA | 1,000,388 | A→C | G391G (GGA→GGC) | elfC → | putative fimbrial usher protein ElfC |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,102,105 | A→G | V8A (GTT→GCT) | csgF ← | curli assembly component |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,155,124 | (A)7→6 | coding (1013/1023 nt) coding (1/642 nt) |
mltG → tmk → |
endolytic murein transglycosylase hypothetical protein |
| RA | 1,176,268 | A→G | N281S (AAC→AGC) | lolC → | lipoprotein release complex ‑ inner membrane subunit |
| RA | 1,207,908 | (G)5→6 | coding (408/630 nt) | ycfK → | e14 prophage; protein StfP |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,222,371 | A→G | A88A (GCT→GCC) | ymgD ← | PF16456 family protein YmgD |
| RA | 1,256,814 | T→C | E333E (GAA→GAG) | ychF ← | redox‑responsive ATPase YchF |
| RA | 1,276,807 | A→G | V271A (GTA→GCA) | narX ← | sensory histidine kinase NarX |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| RA | 1,338,450 | A→G | T874A (ACC→GCC) | acnA → | aconitate hydratase 1 |
| RA | 1,351,196 | (G)7→8 | intergenic (‑157/+211) | fabI ← / ← ycjD | enoyl‑[acyl‑carrier‑protein] reductase/DUF559 domain‑containing protein YcjD |
| RA | 1,432,087 | C→T | G1013G (GGC→GGT) | stfR → | Rac prophage; putative membrane protein |
| RA | 1,471,150 | (A)7→6 | pseudogene (632/3495 nt) | ydbA → | putative outer membrane protein, N‑terminal fragment |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,572,404 | T→C | intergenic (‑359/+3) | gadB ← / ← pqqL | glutamate decarboxylase B/putative zinc peptidase |
| RA | 1,594,256 | (C)8→10 | pseudogene (3831/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,619,496 | (A)6→7 | coding (377/435 nt) | marR → | DNA‑binding transcriptional repressor MarR |
| RA | 1,632,837 | A→G | intergenic (‑552/‑53) | ydfJ ← / → ynfT | putative transporter YdfJ/Qin prophage; protein YnfT |
| RA | 1,634,602 | T→C | E95G (GAA→GGA) | tfaQ ← | Qin prophage; putative tail fiber assembly protein TfaQ |
| RA | 1,634,642 | C→T | G82S (GGC→AGC) | tfaQ ← | Qin prophage; putative tail fiber assembly protein TfaQ |
| RA | 1,659,652 | T→C | I528I (ATT→ATC) | ynfE → | putative selenate reductase YnfE |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,714,326 | (T)9→8 | intergenic (+55/‑51) | dtpA → / → gstA | dipeptide/tripeptide:H(+) symporter DtpA/glutathione S‑transferase GstA |
| RA | 1,724,478 | (G)6→7 | coding (178/522 nt) | sodC ← | superoxide dismutase (Cu‑Zn) |
| RA | 1,728,012 | A→G | Y59C (TAC→TGC) | gloA → | glyoxalase I |
| RA | 1,734,085 | T→C | E6G (GAA→GGA) | grxD ← | glutaredoxin 4 |
| RA | 1,739,481 | A→G | R106R (CGT→CGC) | ydhB ← | putative LysR family DNA‑binding transcriptional regulator YdhB |
| RA | 1,802,766 | T→C | intergenic (‑196/‑328) | thrS ← / → arpB | threonine‑‑tRNA ligase/putative ankyrin repeat protein B, N‑terminal fragment |
| RA | 1,869,980 | A→G | A342A (GCA→GCG) | yeaH → | DUF444 domain‑containing protein YeaH |
| 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 | 1,933,732 | G→A | I291I (ATC→ATT) | edd ← | phosphogluconate dehydratase |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,005,319 | G→A | G6D (GGC→GAC) | fliS → | flagellar biosynthesis protein FliS |
| RA | 2,106,518 | (C)6→7 | coding (709/1167 nt) | wbbH ← | putative O‑antigen polymerase |
| RA | 2,165,573 | (C)6→5 | intergenic (+52/‑95) | yegP → / → yegQ | DUF1508 domain‑containing protein YegP/putative peptidase YegQ |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,229,119 | C→T | intergenic (+54/+319) | yohP → / ← dusC | putative membrane protein YohP/tRNA‑dihydrouridine(16) synthase |
| RA | 2,380,499 | T→C | T49A (ACA→GCA) | menF ← | isochorismate synthase MenF |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,541,754 | G→A | L253L (CTC→CTT) | cysU ← | sulfate/thiosulfate ABC transporter inner membrane subunit CysU |
| RA | 2,646,583 | (G)6→7 | coding (743/2313 nt) | pbpC ← | peptidoglycan glycosyltransferase PbpC |
| RA | 2,695,588 | +A | intergenic (‑45/‑213) | purL ← / → mltF | phosphoribosylformylglycinamide synthetase/membrane‑bound lytic murein transglycosylase F |
| RA | 2,765,794 | (C)7→8 | intergenic (‑18/‑124) | yfjM ← / → rnlA | CP4‑57 prophage; protein YfjM/CP4‑57 prophage; RNase LS, toxin of the RnlAB toxin‑antitoxin system |
| RA | 2,769,648 | (C)6→7 | intergenic (+162/‑55) | yfjQ → / → yfjR | CP4‑57 prophage; protein YfjQ/CP4‑57 prophage; putative DNA‑binding transcriptional regulator |
| RA | 2,808,753 | C→T | pseudogene (438/1178 nt) | ygaY → | putative transporter YgaY, N‑terminal fragment |
| 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 | 2,892,308 | G→A | G32E (GGG→GAG) | queD → | 6‑carboxy‑5,6,7,8‑tetrahydropterin synthase |
| RA | 2,943,150 | T→C | intergenic (‑5/‑187) | ygdI ← / → csdA | DUF903 domain‑containing lipoprotein YgdI/cysteine sulfinate desulfinase |
| RA | 2,947,713 | (T)7→8 | intergenic (+30/+44) | metV → / ← amiC | tRNA‑Met/N‑acetylmuramoyl‑L‑alanine amidase C |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,964,319 | (A)7→6 | intergenic (‑142/+42) | ppdA ← / ← thyA | conserved protein PpdA/thymidylate synthase |
| RA | 2,967,846 | C→T | V197M (GTG→ATG) | ptsP ← | phosphoenolpyruvate‑protein phosphotransferase PtsP |
| RA | 2,999,680 | (G)7→8 | coding (212/756 nt) | ygeR ← | LysM domain‑containing putative peptidase lipoprotein YgeR |
| RA | 2,999,755 | (C)6→7 | coding (137/756 nt) | ygeR ← | LysM domain‑containing putative peptidase lipoprotein YgeR |
| RA | 3,017,609 | A→G | D517G (GAC→GGC) | ygfK → | putative oxidoreductase, Fe‑S subunit |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,101,968 | C→T | A56T (GCC→ACC) | yggL ← | protein YggL |
| RA | 3,102,340 | (C)6→7 | coding (513/720 nt) | trmI ← | tRNA m(7)G46 methyltransferase |
| RA | 3,153,648 | A→G | Y29C (TAC→TGC) | yghB → | DedA family protein YghB |
| RA | 3,186,103 | G→C | intergenic (+8/‑84) | yqiG → / → insC‑5 | putative outer membrane usher protein YqiG/IS2 insertion element repressor InsA |
| RA | 3,200,486 | T→C | E160E (GAA→GAG) | ygiF ← | inorganic triphosphatase |
| RA | 3,322,459 | A→G | L16P (CTT→CCT) | secG ← | Sec translocon subunit SecG |
| RA | 3,332,350 | A→G | V129A (GTT→GCT) | yhbE ← | inner membrane protein YhbE |
| 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 | 3,418,852 | G→T | intergenic (+241/‑190) | yhdV → / → yhdW | lipoprotein YhdV/putative ABC transporter periplasmic binding protein YhdW |
| RA | 3,474,817 | (G)5→4 | coding (149/288 nt) | tusB ← | sulfurtransferase complex subunit TusB |
| RA | 3,496,567 | A→C | D6A (GAC→GCC) | nirD → | nitrite reductase subunit NirD |
| RA | 3,522,499 | A→G | S85P (TCA→CCA) | hofM ← | DNA utilization protein HofM |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,582,425 | T→C | V188A (GTA→GCA) | yhhZ → | putative endonuclease YhhZ |
| RA | 3,599,887 | (A)5→6 | intergenic (‑229/+42) | livJ ← / ← rpoH | branched chain amino acid/phenylalanine ABC transporter periplasmic binding protein/RNA polymerase, sigma 32 (sigma H) factor |
| RA | 3,714,532 | C→T | W621* (TGG→TGA) | bisC ← | biotin sulfoxide reductase |
| RA | 3,784,538 | G→A | intergenic (‑96/+46) | grxC ← / ← yibN | glutaredoxin 3/putative sulfurtransferase YibN |
| 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 | 4,077,754 | C→T | G102G (GGC→GGT) | yiiD → | putative acetyltransferase YiiD |
| RA | 4,157,174 | C→T | R109C (CGT→TGT) | argH → | argininosuccinate lyase |
| RA | 4,178,857 | C→T | G137G (GGC→GGT) | rplK → | 50S ribosomal subunit protein L11 |
| RA | 4,279,113 | G→C | G212A (GGT→GCT) | ghxP → | guanine/hypoxanthine transporter GhxP |
| RA | 4,282,493 | C→T | E195K (GAA→AAA) | yjcF ← | pentapeptide repeat‑containing protein YjcF |
| RA | 4,292,906 | A→G | A465A (GCA→GCG) | 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 |
| RA | 4,412,691 | T→C | V102A (GTT→GCT) | yjfM → | DUF1190 domain‑containing protein YjfM |
| RA | 4,422,430 | A→G | D82G (GAC→GGC) | ulaD → | 3‑keto‑L‑gulonate‑6‑phosphate decarboxylase UlaD |
| RA | 4,424,457 | (A)8→9 | intergenic (+71/+59) | ulaF → / ← yjfY | L‑ribulose‑5‑phosphate 4‑epimerase UlaF/DUF1471 domain‑containing protein YjfY |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,473,680 | C→T | G125E (GGG→GAG) | bdcA ← | c‑di‑GMP‑binding biofilm dispersal mediator protein |
| RA | 4,488,579 | (C)7→8 | coding (1485/1503 nt) | yjgR ← | DUF853 domain‑containing protein YjgR |
| RA | 4,492,988 | A→G | F122L (TTC→CTC) | idnO ← | 5‑keto‑D‑gluconate 5‑reductase |
| RA | 4,516,058 | T→C | Y207C (TAC→TGC) | fecA ← | ferric citrate outer membrane transporter |
| RA | 4,558,126 | A→G | V55A (GTT→GCT) | hypT ← | DNA‑binding transcriptional dual regulator HypT |
| RA | 4,606,094 | (G)8→7 | noncoding (72/87 nt) | leuV ← | tRNA‑Leu |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1632858–1632901 | 1633548–1633229 | 329–691 | 16 [10] | [12] 13 | ynfT–ydfK | ynfT,ydfK |
| * | * | ÷ | NC_000913 | 3423755–3424234 | 3424525–3424239 | 6–771 | 15 [10] | [8] 14 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 7 (0.130) | 82 (1.700) | 49/244 | 0.0 | 91.0% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 10 (0.210) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 7 (0.130) | 38 (0.790) | 26/244 | 0.7 | 82.4% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 10 (0.210) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 3363001 = | 82 (1.500) | 80 (1.480) | 52/274 | 0.1 | 66.0% | 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) | 61 (1.120) | 43/276 | 0.2 | 93.8% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 4 (0.070) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||