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 | 30,005 | A→G | T119A (ACG→GCG) | carA → | carbamoyl phosphate synthetase subunit alpha |
| RA | 96,560 | A→G | T187A (ACT→GCT) | mraY → | phospho‑N‑acetylmuramoyl‑pentapeptide‑ transferase |
| RA | 128,172 | T→C | R87R (CGT→CGC) | lpd → | lipoamide dehydrogenase |
| RA | 130,488 | T→C | N258S (AAC→AGC) | yacH ← | DUF3300 domain‑containing protein YacH |
| RA | 131,619 | T→C | L2P (CTA→CCA) | acnB → | hypothetical protein |
| RA | 151,329 | T→C | T91A (ACT→GCT) | yadK ← | putative fimbrial protein YadK |
| RA | 156,242 | T→C | intergenic (‑41/+57) | yadV ← / ← yadN | putative fimbrial chaperone YadV/putative fimbrial protein YadN |
| RA | 156,995 | A→G | intergenic (‑112/+258) | yadN ← / ← folK | putative fimbrial protein YadN/2‑amino‑4‑hydroxy‑6‑ hydroxymethyldihydropteridine diphosphokinase |
| RA | 198,312 | A→G | T129A (ACC→GCC) | bamA → | outer membrane protein assembly factor BamA |
| RA | 216,145 | (C)6→7 | intergenic (+166/+34) | nlpE → / ← yaeF | lipoprotein NlpE/peptidase C92 family protein |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 264,878 | A→G | V110A (GTC→GCC) | yafX ← | CP4‑6 prophage; protein YafX |
| RA | 303,948 | A→G | S79P (TCC→CCC) | ykgJ ← | putative zinc‑ or iron‑chelating domain‑containing protein YkgJ |
| RA | 380,022 | (G)10→9 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 391,508 | C→T | pseudogene (1258/1458 nt) | yaiT → | putative autotransporter YaiT |
| RA | 468,271 | (T)8→7 | intergenic (+41/‑112) | cof → / → decR | HMP‑PP phosphatase/DNA‑binding transcriptional activator DecR |
| RA | 520,655 | G→A | K80K (AAG→AAA) | ybbP → | putative ABC transporter membrane subunit YbbP |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 578,458 | (C)6→7 | coding (352/462 nt) coding (132/183 nt) |
rzpD → rzoD → |
DLP12 prophage; putative prophage endopeptidase RzpD DLP12 prophage; putative prophage lysis lipoprotein RzoD |
| RA | 651,234 | A→G | V208A (GTG→GCG) | citC ← | citrate lyase synthetase |
| RA | 706,799 | A→G | D236G (GAC→GGC) | glnS → | glutamine‑‑tRNA ligase |
| RA | 802,151 | A→G | T89A (ACC→GCC) | ybhI → | putative tricarboxylate transporter |
| RA | 839,239 | Δ1 bp | intergenic (‑32/+10) | ybiX ← / ← fiu | PKHD‑type hydroxylase YbiX/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 | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 943,384 | T→C | V809A (GTT→GCT) | dmsA → | dimethyl sulfoxide reductase subunit A |
| RA | 968,542 | C→T | N59N (AAC→AAT) | lpxK → | tetraacyldisaccharide 4'‑kinase |
| RA | 999,703 | T→C | V163A (GTC→GCC) | elfC → | putative fimbrial usher protein ElfC |
| RA | 1,000,776 | C→T | Q521* (CAA→TAA) | 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 | 1,039,878 | G→A | V195M (GTG→ATG) | appB → | cytochrome bd‑II ubiquinol oxidase subunit II |
| RA | 1,066,765 | A→G | D394G (GAC→GGC) | agp → | glucose‑1‑phosphatase |
| RA | 1,097,218 | (G)7→8 | intergenic (+389/+347) | ycdU → / ← serX | uncharacterized protein YcdU/tRNA‑Ser |
| RA | 1,102,635 | Δ1 bp | coding (562/651 nt) | csgD ← | DNA‑binding transcriptional dual regulator CsgD |
| RA | 1,103,745 | (T)7→8 | intergenic (‑549/‑206) | csgD ← / → csgB | DNA‑binding transcriptional dual regulator CsgD/curlin, minor subunit |
| RA | 1,115,363 | T→C | Q43R (CAG→CGG) | mdtG ← | efflux pump MdtG |
| RA | 1,141,920 | A→G | R816R (CGT→CGC) | rne ← | ribonuclease E |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| 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 | 1,212,088 | (C)8→9 | intergenic (‑85/+172) | iraM ← / ← ymgK | anti‑adaptor protein IraM, inhibitor of sigma(S) proteolysis/protein YmgK |
| RA | 1,220,698 | A→G | pseudogene (1098/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,254,839 | A→G | W372R (TGG→CGG) | ycgV ← | putative autotransporter adhesin YcgV |
| RA | 1,295,663 | A→G | V820A (GTT→GCT) | adhE ← | aldehyde‑alcohol dehydrogenase |
| RA | 1,359,437 | C→T | intergenic (‑96/+53) | ymjE ← / ← puuA | protein YmjE/glutamate‑putrescine ligase |
| RA | 1,361,497 | T→C | G126G (GGT→GGC) | puuD → | gamma‑glutamyl‑gamma‑aminobutyrate hydrolase |
| RA | 1,396,138 | C→T | D21D (GAC→GAT) | insH‑4 → | IS5 transposase and trans‑activator |
| RA | 1,487,297 | A→G | G21G (GGA→GGG) | ydcF → | DUF218 domain‑containing protein YdcF |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,553,841 | T→C | intergenic (‑3/+131) | adhP ← / ← maeA | ethanol dehydrogenase/alcohol dehydrogenase/malate dehydrogenase, NAD‑requiring |
| RA | 1,559,004 | A→G | V5A (GTT→GCT) | ddpD ← | putative D,D‑dipeptide ABC transporter ATP‑binding subunit DdpD |
| RA | 1,594,256 | (C)8→7 | pseudogene (3831/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,606,161 | (A)7→8 | coding (62/876 nt) | lsrF → | 3‑hydroxy‑2,4‑pentadione 5‑phosphate thiolase |
| RA | 1,634,642 | C→T | G82S (GGC→AGC) | tfaQ ← | Qin prophage; putative tail fiber assembly protein TfaQ |
| RA | 1,650,397 | A→G | pseudogene (320/921 nt) | ydfE → | Qin prophage; protein YdfE |
| 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 | 1,784,980 | A→G | G711G (GGT→GGC) | ppsA ← | phosphoenolpyruvate synthetase |
| RA | 1,846,485 | C→T | C159Y (TGC→TAC) | topB ← | DNA topoisomerase III |
| RA | 1,861,531 | A→G | intergenic (‑199/+171) | ydjL ← / ← yeaC | putative zinc‑binding dehydrogenase YdjL/conserved protein YeaC |
| RA | 1,868,816 | T→C | Y637H (TAT→CAT) | yeaG → | protein kinase YeaG |
| 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 | 1,906,768 | T→C | Y98C (TAT→TGT) | rlmA ← | 23S rRNA m(1)G745 methyltransferase |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 1,988,106 | (C)6→7 | intergenic (‑147/‑116) | azuC ← / → yecR | uncharacterized protein AzuC/lipoprotein YecR |
| RA | 1,996,183 | T→C | N217S (AAC→AGC) | sdiA ← | DNA‑binding transcriptional dual regulator SdiA |
| RA | 1,998,273 | T→C | A69A (GCA→GCG) | tcyL ← | cystine ABC transporter membrane subunit |
| RA | 2,040,590 | T→A | G36G (GGT→GGA) | msrQ → | periplasmic protein‑L‑methionine sulfoxide reductase heme binding subunit |
| RA | 2,052,343 | (T)6→7 | pseudogene (986/1053 nt) | yeeL ← | putative glycosyltransferase, N‑terminal fragment |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,176,220 | A→T | D34E (GAT→GAA) | gatZ ← | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatZ |
| RA | 2,215,832 | (C)5→6 | coding (645/732 nt) | yehW ← | glycine betaine ABC transporter membrane subunit YehW |
| RA | 2,225,487 | T→C | T49A (ACA→GCA) | yohC ← | putative inner membrane protein |
| RA | 2,238,134 | T→C | T386A (ACC→GCC) | mglA ← | D‑galactose/methyl‑galactoside ABC transporter ATP binding subunit |
| RA | 2,239,742 | T→C | T203A (ACC→GCC) | mglB ← | D‑galactose/methyl‑galactoside ABC transporter periplasmic binding protein |
| RA | 2,329,217 | A→G | V194A (GTG→GCG) | yfaQ ← | tandem DUF2300 domain‑containing protein YfaQ |
| RA | 2,416,105 | T→C | G453G (GGT→GGC) | pta → | phosphate acetyltransferase |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,463,534 | T→C | Y175H (TAC→CAC) | yfdF → | protein YfdF |
| RA | 2,479,327 | T→C | V42V (GTT→GTC) | dsdA → | D‑serine ammonia‑lyase |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,530,730 | T→C | E168E (GAA→GAG) | zipA ← | cell division protein ZipA |
| RA | 2,539,061 | T→C | T175A (ACG→GCG) | cysM ← | cysteine synthase B |
| RA | 2,634,255 | A→G | A8A (GCA→GCG) | xseA → | exodeoxyribonuclease VII subunit XseA |
| RA | 2,662,801 | T→C | T175A (ACG→GCG) | trmJ ← | tRNA Cm32/Um32 methyltransferase |
| RA | 2,672,469 | G→A | L141L (CTG→CTA) | hcaD → | putative 3‑phenylpropionate/cinnamate dioxygenase ferredoxin reductase subunit |
| RA | 2,679,099 | G→A | A90V (GCC→GTC) | yphF ← | putative ABC transporter periplasmic binding protein YphF |
| RA | 2,681,511 | T→C | H412R (CAC→CGC) | yphG ← | DUF5107 domain‑containing protein YphG |
| RA | 2,689,289 | T→C | Y73C (TAC→TGC) | qseG ← | outer membrane lipoprotein QseG |
| RA | 2,709,734 | T→C | P93P (CCA→CCG) | rpoE ← | RNA polymerase sigma E factor |
| RA | 2,777,249 | T→C | C45C (TGT→TGC) | yfjZ → | CP4‑57 prophage; putative antitoxin of the YpjF‑YfjZ toxin‑antitoxin system |
| RA | 2,806,550 | C→T | R181C (CGT→TGT) | proW → | glycine betaine ABC transporter membrane subunit ProW |
| 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 | 2,867,926 | (C)6→8 | coding (828/1140 nt) | nlpD ← | murein hydrolase activator NlpD |
| RA | 2,895,500 | T→C | T94A (ACC→GCC) | ygcQ ← | putative flavoprotein |
| RA | 2,901,662 | T→C | G357G (GGT→GGC) | yqcE → | putative transport protein YqcE |
| RA | 2,910,512 | T→C | E58E (GAA→GAG) | mazG ← | nucleoside triphosphate pyrophosphohydrolase |
| RA | 2,915,444 | A→T | I130F (ATC→TTC) | barA → | sensory histidine kinase BarA |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 3,001,304 | (G)7→9 | coding (960/2259 nt) | xdhA → | putative xanthine dehydrogenase molybdenum‑binding subunit XdhA |
| RA | 3,033,930 | C→T | E415E (GAG→GAA) | lysS ← | lysine‑‑tRNA ligase, constitutive |
| RA | 3,062,255 | T→C | V469A (GTA→GCA) | scpA → | methylmalonyl‑CoA mutase |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,206,750 | A→G | I96M (ATA→ATG) | ttdA → | L(+)‑tartrate dehydratase subunit alpha |
| RA | 3,280,275 | T→C | V20A (GTT→GCT) | agaV → | N‑acetyl‑D‑galactosamine specific PTS enzyme IIB component |
| RA | 3,350,991 | G→A | P679S (CCG→TCG) | arcB ← | sensory histidine kinase ArcB |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,355,610 | G→A | D296N (GAT→AAT) | gltB → | glutamate synthase subunit GltB |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,524,569 | T→C | S567P (TCC→CCC) | mrcA → | peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcA |
| RA | 3,529,992 | T→C | G73G (GGT→GGC) | hslO → | molecular chaperone Hsp33 |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,584,131 | T→A | L152Q (CTG→CAG) | insB‑6 → | IS1 protein InsB |
| RA | 3,630,810 | A→G | intergenic (‑208/+158) | yhiI ← / ← yhiJ | putative membrane fusion protein YhiI/DUF4049 domain‑containing protein YhiJ |
| RA | 3,638,502 | T→C | A287A (GCT→GCC) | pitA → | metal phosphate:H(+) symporter PitA |
| RA | 3,693,045 | A→T | I731N (ATC→AAC) | bcsA ← | cellulose synthase catalytic subunit |
| RA | 3,805,423 | G→A | G176G (GGC→GGT) | waaP ← | lipopolysaccharide core heptose (I) kinase |
| 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 | 3,889,260 | A→G | E177E (GAA→GAG) | tnaA → | tryptophanase |
| RA | 4,021,013 | A→G | N263S (AAC→AGC) | ubiB → | ubiquinone biosynthesis protein UbiB |
| RA | 4,037,929 | (G)6→7 | noncoding (411/2905 nt) | rrlA → | 23S ribosomal RNA |
| RA | 4,242,517 | A→G | intergenic (‑263/+109) | xylE ← / ← malG | D‑xylose:H(+) symporter/maltose ABC transporter membrane subunit MalG |
| RA | 4,277,527 | G→A | R20H (CGC→CAC) | soxR → | DNA‑binding transcriptional dual regulator SoxR |
| RA | 4,280,591 | T→C | G204G (GGT→GGC) | yjcE → | putative transporter YjcE |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,310,039 | T→C | K314K (AAA→AAG) | alsA ← | D‑allose ABC transporter ATP binding subunit |
| RA | 4,403,153 | T→C | G372G (GGT→GGC) | hflK → | regulator of FtsH protease |
| RA | 4,420,831 | G→A | T284T (ACG→ACA) | ulaA → | L‑ascorbate specific PTS enzyme IIC component |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,489,240 | +G | coding (824/1503 nt) | yjgR ← | DUF853 domain‑containing protein YjgR |
| RA | 4,550,142 | C→T | P385P (CCG→CCA) | gntP ← | fructuronate transporter |
| RA | 4,561,411 | G→A | G161D (GGC→GAC) | kptA → | RNA 2'‑phosphotransferase |
| RA | 4,595,581 | A→G | F91L (TTT→CTT) | lgoR ← | putative DNA‑binding transcriptional regulator LgoR |
| RA | 4,606,094 | (G)8→7 | noncoding (72/87 nt) | leuV ← | tRNA‑Leu |
| RA | 4,631,331 | T→C | V200A (GTA→GCA) | slt → | soluble lytic murein transglycosylase |
| RA | 4,639,572 | (T)8→7 | intergenic (+42/+18) | creD → / ← arcA | putative inner membrane protein/DNA‑binding transcriptional dual regulator ArcA |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196275 | 1211437 | 15163 | 27 [24] | [24] 29 | [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 | 2520971–2520986 | 2521090–2521051 | 66–120 | 28 [26] | [24] 32 | [valU]–[valX] | [valU],[valX] |
| * | * | ÷ | NC_000913 | 3423770–3424233 | 3424535–3424239 | 7–766 | 27 [14] | [25] 29 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 374921 = | NA (NA) | 66 (1.010) | 19/190 | 2.0 | NA | intergenic (+40/‑538) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377531 = | NA (NA) | intergenic (+220/+4) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 374963 | NA (NA) | 58 (0.880) | 25/190 | 1.2 | 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) | 54 (0.720) | 17/216 | 2.8 | NA | noncoding (17/36 nt) | other | REP31d |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 375203 = | NA (NA) | 66 (0.880) | 28/216 | 1.3 | NA | noncoding (17/36 nt) | other | REP31f |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 79 (0.850) | 57/268 | 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 = | 132 (1.380) | 130 (1.370) | 73/274 | 0.1 | 66.5% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 0 (0.000) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 113 (1.180) | 63/276 | 0.2 | 99.1% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 1 (0.010) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||