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 | 137,955 | A→G | K291K (AAA→AAG) | cueO → | cuprous oxidase/multicopper oxidase with role in copper homeostasis |
| RA | 139,481 | A→G | V582A (GTC→GCC) | gcd ← | quinoprotein glucose dehydrogenase |
| RA | 139,693 | T→C | A511A (GCA→GCG) | gcd ← | quinoprotein glucose dehydrogenase |
| RA | 187,607 | A→G | R348R (CGT→CGC) | glnD ← | PII uridylyltransferase/uridylyl removing enzyme |
| RA | 235,181 | G→A | W122* (TGG→TGA) | yafS → | putative S‑adenosyl‑L‑methionine‑dependent methyltransferase |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 267,888 | A→G | S40P (TCC→CCC) | yafZ ← | CP4‑6 prophage; conserved protein YafZ |
| RA | 282,311 | C→T | P12S (CCC→TCC) | yagE → | CP4‑6 prophage; putative 2‑keto‑3‑deoxygluconate aldolase |
| RA | 432,249 | A→G | intergenic (‑236/+63) | tsx ← / ← yajI | nucleoside‑specific channel‑forming protein Tsx/putative lipoprotein YajI |
| RA | 445,396 | A→G | V424A (GTG→GCG) | yajR ← | putative major facilitator superfamily transport protein YajR |
| RA | 513,158 | T→C | F195L (TTC→CTC) | ybaT → | putative transporter YbaT |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 543,854 | T→C | T65A (ACA→GCA) | allE ← | (S)‑ureidoglycine aminohydrolase |
| RA | 581,723 | C→T | H64Y (CAT→TAT) | tfaD → | DLP12 prophage; putative tail fiber assembly protein TfaD |
| RA | 605,175 | A→G | F84L (TTC→CTC) | nfsB ← | NAD(P)H nitroreductase NfsB |
| RA | 627,340 | A→G | Y424C (TAC→TGC) | entE → | 2,3‑dihydroxybenzoate‑AMP ligase |
| RA | 644,981 | G→A | A8V (GCC→GTC) | rna ← | RNase I |
| RA | 645,483 | A→G | G366G (GGT→GGC) | citT ← | citrate:succinate antiporter |
| RA | 709,873 | T→C | R28R (CGT→CGC) | chiQ → | lipoprotein ChiQ |
| RA | 816,176 | T→C | T158A (ACT→GCT) | ybhK ← | putative transferase YbhK |
| RA | 834,209 | A→G | V380V (GTA→GTG) | dinG → | ATP‑dependent DNA helicase DinG |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 925,047 | A→G | D595G (GAC→GGC) | 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 | 951,624 | C→T | G644D (GGT→GAT) | pflB ← | pyruvate formate‑lyase |
| RA | 955,039 | A→G | Y532H (TAC→CAC) | ycaO ← | ribosomal protein S12 methylthiotransferase accessory factor YcaO |
| RA | 1,004,562 | A→G | S206G (AGC→GGC) | ycbF → | putative fimbrial chaperone YcbF |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,041,533 | C→T | P306L (CCG→CTG) | appA → | periplasmic phosphoanhydride phosphatase/multiple inositol‑polyphosphate phosphatase |
| RA | 1,041,690 | A→G | E358E (GAA→GAG) | appA → | periplasmic phosphoanhydride phosphatase/multiple inositol‑polyphosphate phosphatase |
| RA | 1,052,496 | C→T | P289P (CCG→CCA) | yccM ← | putative 4Fe‑4S membrane protein |
| RA | 1,097,037 | (G)7→8 | intergenic (+208/+528) | ycdU → / ← serX | uncharacterized protein YcdU/tRNA‑Ser |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,157,814 | (C)6→7 | intergenic (+240/‑55) | ycfH → / → ptsG | putative metal‑dependent hydrolase YcfH/glucose‑specific PTS enzyme IIBC component |
| RA | 1,177,187 | A→G | E190G (GAA→GGA) | lolD → | lipoprotein release complex ‑ ATP binding subunit |
| RA | 1,192,484 | A→G | S50P (TCG→CCG) | hflD ← | lysogenization regulator |
| 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 | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,248,432 | A→G | L228P (CTG→CCG) | dhaM ← | dihydroxyacetone kinase subunit M |
| RA | 1,356,391 | A→G | G240G (GGT→GGC) | sapA ← | putative periplasmic binding protein SapA |
| RA | 1,466,196 | A→G | pseudogene (805/2518 nt) | ydbA → | putative outer membrane protein, N‑terminal fragment |
| RA | 1,486,664 | G→A | G1202S (GGC→AGC) | hrpA → | ATP‑dependent RNA helicase HrpA |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,554,493 | T→C | T393A (ACC→GCC) | maeA ← | malate dehydrogenase, NAD‑requiring |
| RA | 1,562,458 | A→G | R8R (CGT→CGC) | ddpA ← | putative D,D‑dipeptide ABC transporter periplasmic binding protein |
| RA | 1,594,132 | (C)8→9 | 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 | 1,594,479 | A→G | pseudogene (3608/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,634,642 | C→T | G82S (GGC→AGC) | tfaQ ← | Qin prophage; putative tail fiber assembly protein TfaQ |
| RA | 1,660,373 | A→G | N769D (AAT→GAT) | ynfE → | putative selenate reductase YnfE |
| RA | 1,663,793 | T→C | V62A (GTC→GCC) | ynfH → | putative menaquinol dehydrogenase |
| RA | 1,665,769 | C→G | A152G (GCC→GGC) | clcB → | putative chloride:H(+) antiporter ClcB |
| RA | 1,678,734 | T→C | V103A (GTA→GCA) | ydgH → | DUF1471 domain‑containing protein YdgH |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,726,337 | T→C | G105G (GGT→GGC) | nemR → | DNA‑binding transcriptional repressor NemR |
| RA | 1,760,542 | C→T | R417Q (CGG→CAG) | sufD ← | Fe‑S cluster scaffold complex subunit SufD |
| RA | 1,771,556 | G→A | W162* (TGG→TGA) | ydiM → | putative exporter YdiM |
| RA | 1,774,056 | (G)5→6 | coding (268/867 nt) | ydiB → | shikimate dehydrogenase/quinate dehydrogenase |
| RA | 1,811,302 | T→C | G123G (GGT→GGC) | tcyP → | cystine/sulfocysteine:cation symporter |
| RA | 1,845,814 | C→T | A383T (GCC→ACC) | 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 | 1,944,415 | T→C | T314T (ACA→ACG) | ruvB ← | Holliday junction branch migration complex subunit RuvB |
| RA | 1,976,988 | C→T | G51D (GGC→GAC) | motA ← | motility protein A |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 1,983,101 | T→C | Y147C (TAC→TGC) | araH ← | arabinose ABC transporter membrane subunit |
| RA | 1,988,905 | A→G | T64A (ACC→GCC) | ftnA → | ferritin iron storage protein |
| RA | 1,997,280 | G→A | L179L (CTG→TTG) | tcyN ← | cystine ABC transporter ATP binding subunit |
| RA | 2,056,328 | T→C | L423P (CTA→CCA) | amn → | AMP nucleosidase |
| RA | 2,068,240 | T→C | intergenic (‑919/‑395) | insH‑6 ← / → yoeA | CP4‑44 prophage; IS5 transposase and trans‑activator/CP4‑44 prophage; TonB‑dependent receptor plug domain‑containing protein YoeA |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,177,197 | A→G | V3A (GTG→GCG) | gatY ← | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY |
| RA | 2,207,404 | T→C | A570A (GCT→GCC) | yehM → | putative YehN |
| RA | 2,267,780 | (T)6→7 | intergenic (+69/‑49) | yeiQ → / → yeiR | putative dehydrogenase, NAD‑dependent/zinc‑binding GTPase YeiR |
| RA | 2,275,146 | T→C | V323A (GTC→GCC) | yejB → | putative oligopeptide ABC transporter membrane subunit YejB |
| RA | 2,288,561 | (C)7→6 | pseudogene (354/2525 nt) | yejO ← | adhesin‑like autotransporter YejO |
| RA | 2,385,750 | A→G | intergenic (‑28/‑110) | yfbK ← / → yfbL | IPR002035/DUF3520 domain‑containing protein YfbK/putative peptidase YfbL |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,447,796 | A→G | D215D (GAT→GAC) | prmB ← | 50S ribosomal subunit protein L3 N(5)‑glutamine methyltransferase |
| RA | 2,467,324 | G→A | M260I (ATG→ATA) | intS → | CPS‑53 (KpLE1) prophage; prophage CPS‑53 integrase |
| RA | 2,492,338 | A→G | F306S (TTC→TCC) | frc ← | formyl‑CoA transferase |
| RA | 2,497,609 | T→C | V229V (GTA→GTG) | alaC ← | glutamate‑‑pyruvate aminotransferase AlaC |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,633,920 | T→C | T51A (ACC→GCC) | guaB ← | inosine 5'‑monophosphate dehydrogenase |
| RA | 2,638,026 | (C)6→5 | coding (627/1179 nt) | bamB ← | outer membrane protein assembly factor BamB |
| RA | 2,648,538 | C→T | E1250E (GAG→GAA) | yfhM ← | alpha2‑macroglobulin |
| RA | 2,676,481 | G→A | G115G (GGC→GGT) | yphD ← | putative ABC transporter membrane subunit YphD |
| RA | 2,771,340 | C→T | H65Y (CAC→TAC) | yfjT → | CP4‑57 prophage; uncharacterized protein YfjT |
| RA | 2,775,907 | G→A | intergenic (+91/‑12) | ypjI → / → yfjX | putative UPF0401 protein YpjI/CP4‑57 prophage; putative antirestriction protein |
| RA | 2,787,193 | G→A | pseudogene (797/2253 nt) | ygaQ → | putative uncharacterized protein YgaQ |
| RA | 2,792,331 | (CG)4→3 | coding (1059‑1060/1449 nt) | gabD → | NADP(+)‑dependent succinate‑semialdehyde dehydrogenase |
| RA | 2,794,105 | T→C | intergenic (+90/‑148) | gabT → / → gabP | 4‑aminobutyrate aminotransferase GabT/4‑aminobutyrate:H(+) symporter |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| RA | 2,815,090 | A→G | R450R (CGT→CGC) | gshA ← | glutamate‑‑cysteine ligase |
| RA | 2,849,499 | T→C | P117P (CCA→CCG) | hycB ← | formate hydrogenlyase subunit HycB |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,966,866 | A→G | R523R (CGT→CGC) | ptsP ← | phosphoenolpyruvate‑protein phosphotransferase PtsP |
| RA | 3,017,592 | T→C | C511C (TGT→TGC) | ygfK → | putative oxidoreductase, Fe‑S subunit |
| RA | 3,025,506 | A→G | I386V (ATC→GTC) | xanQ → | xanthine:H(+) symporter XanQ |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,099,633 | A→G | intergenic (‑68/+49) | yggM ← / ← ansB | DUF1202 domain‑containing protein YggM/L‑asparaginase 2 |
| RA | 3,165,926 | G→A | N16N (AAC→AAT) | parC ← | DNA topoisomerase IV subunit A |
| RA | 3,194,890 | (A)8→9 | intergenic (‑25/+207) | sibD ← / ← sibE | small RNA SibD/small RNA SibE |
| RA | 3,229,057 | A→T | D57V (GAT→GTT) | ygjK → | glycoside hydrolase |
| RA | 3,281,767 | T→C | intergenic (+142/‑209) | agaA → / → agaS | putative truncated N‑acetylgalactosamine‑6‑phosphate deacetylase/putative galactosamine‑6‑phosphate deaminase/isomerase |
| RA | 3,303,774 | Δ1 bp | coding (327/1008 nt) | yhbW → | putative luciferase‑like monooxygenase |
| RA | 3,304,826 | +G | coding (992/1245 nt) | mtr ← | tryptophan:H(+) symporter Mtr |
| 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 | 3,409,489 | T→C | G140G (GGT→GGC) | prmA → | methyltransferase for 50S ribosomal subunit protein L11 |
| RA | 3,411,691 | A→G | E13E (GAA→GAG) | yhdJ → | DNA adenine methyltransferase |
| RA | 3,418,586 | T→C | M66T (ATG→ACG) | yhdV → | lipoprotein YhdV |
| RA | 3,452,342 | A→G | G195G (GGT→GGC) | rplC ← | 50S ribosomal subunit protein L3 |
| RA | 3,504,478 | T→C | F143L (TTT→CTT) | frlR → | putative DNA‑binding transcriptional regulator FrlR |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,595,056 | T→C | Y142C (TAC→TGC) | livM ← | branched chain amino acid/phenylalanine ABC transporter membrane subunit LivM |
| RA | 3,600,218 | T→C | D189G (GAT→GGT) | rpoH ← | RNA polymerase, sigma 32 (sigma H) factor |
| RA | 3,608,461 | A→G | M671V (ATG→GTG) | zntA → | Zn(2(+))/Cd(2(+))/Pb(2(+)) exporting P‑type ATPase |
| RA | 3,622,965 | T→C | C1258C (TGT→TGC) | rhsB → | rhs element protein RhsB |
| RA | 3,710,903 | T→C | T369A (ACC→GCC) | yhjX ← | putative pyruvate transporter |
| RA | 3,785,332 | A→G | N25D (AAC→GAC) | gpmM → | 2,3‑bisphosphoglycerate‑independent phosphoglycerate mutase |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,832,482 | T→C | T686A (ACG→GCG) | yicI ← | alpha‑D‑xyloside xylohydrolase |
| RA | 3,841,383 | C→T | G119G (GGG→GGA) | nepI ← | purine ribonucleoside exporter |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 3,870,550 | T→C | Y394C (TAC→TGC) | dgoT ← | putative D‑galactonate transporter |
| RA | 3,878,672 | T→C | Y483C (TAC→TGC) | gyrB ← | DNA gyrase subunit B |
| RA | 3,893,684 | T→C | L307S (TTA→TCA) | yidZ → | putative LysR‑type transcriptional regulator YidZ |
| RA | 3,960,231 | C→T | pseudogene (230/449 nt) | yifN ← | putative toxin YifN |
| RA | 3,975,554 | A→G | T137A (ACC→GCC) | wecE → | dTDP‑4‑dehydro‑6‑deoxy‑D‑glucose transaminase |
| RA | 3,977,855 | (G)6→7 | coding (331/1080 nt) | rffT → | 4‑acetamido‑4,6‑dideoxy‑D‑galactose transferase |
| RA | 4,045,892 | A→G | C237C (TGT→TGC) | yihG ← | putative acyltransferase YihG |
| RA | 4,081,668 | A→G | F65L (TTT→CTT) | fdoI ← | formate dehydrogenase O subunit gamma |
| RA | 4,086,811 | Δ1 bp | coding (796/834 nt) | fdhD → | sulfurtransferase for molybdenum cofactor sulfuration |
| RA | 4,195,882 | A→G | V73A (GTC→GCC) | thiC ← | phosphomethylpyrimidine synthase |
| RA | 4,253,791 | A→G | N259S (AAC→AGC) | ubiA → | 4‑hydroxybenzoate octaprenyltransferase |
| RA | 4,257,110 | (G)5→6 | intergenic (+105/‑5) | dgkA → / → lexA | diacylglycerol kinase/DNA‑binding transcriptional repressor LexA |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,304,220 | G→A | Q62* (CAG→TAG) | ytcA ← | putative lipoprotein YtcA |
| RA | 4,371,919 | A→G | T299A (ACC→GCC) | groL → | chaperonin GroEL |
| RA | 4,409,607 | G→A | A111A (GCG→GCA) | rlmB → | 23S rRNA 2'‑O‑ribose G2251 methyltransferase |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,454,776 | C→T | P278P (CCG→CCA) | fbp ← | fructose‑1,6‑bisphosphatase 1 |
| RA | 4,482,321 | A→G | V506A (GTA→GCA) | valS ← | valine‑‑tRNA ligase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196275 | 1211435 | 15161 | 15 [12] | [14] 15 | [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 | 1632687–1632734 | 1634094–1633925 | 1192–1408 | 16 [14] | [14] 17 | ynfT–[pinQ] | ynfT,ydfK,[pinQ] |
| * | * | ÷ | NC_000913 | 3423765–3424230 | 3424525–3424238 | 9–761 | 16 [14] | [12] 16 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 374963 | NA (NA) | 11 (0.280) | 9/190 | 2.5 | NA | noncoding (33/34 nt) | other | REP31a |
| ? | NC_000913 | = 377487 | NA (NA) | intergenic (+176/+48) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 375102 = | NA (NA) | 19 (0.430) | 10/216 | 2.7 | NA | noncoding (17/36 nt) | other | REP31d |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 50 (0.910) | 37/268 | 0.4 | 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 = | 80 (1.410) | 110 (1.950) | 64/274 | 0.0 | 73.2% | 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) | 67 (1.180) | 42/276 | 0.3 | 98.5% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 1 (0.020) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||