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 | 4,415 | G→T | E228* (GAA→TAA) | thrC → | threonine synthase |
| RA | 36,533 | A→G | V431A (GTC→GCC) | caiC ← | carnitine‑CoA ligase |
| RA | 54,578 | A→G | V42A (GTT→GCT) | surA ← | peptidyl‑prolyl cis‑trans isomerase SurA |
| RA | 226,552 | A→G | noncoding (794/2904 nt) | rrlH → | 23S ribosomal RNA |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 272,657 | T→C | intergenic (+3/‑190) | eyeA → / → ykfC | CP4‑6 prophage; small RNA EyeA/CP4‑6 prophage; PF00078 domain‑containing protein YkfC |
| RA | 282,228 | A→G | intergenic (‑245/‑50) | yagA ← / → yagE | CP4‑6 prophage; integrase core domain‑containing protein YagA/CP4‑6 prophage; putative 2‑keto‑3‑deoxygluconate aldolase |
| RA | 292,968 | T→C | intergenic (‑20/+252) | yagK ← / ← yagL | CP4‑6 prophage; uncharacterized protein YagK/CP4‑6 prophage; resolvase‑like catalytic domain‑containing protein YagL |
| RA | 299,871 | (G)5→6 | coding (1064/2199 nt) | paoC ← | aldehyde dehydrogenase: molybdenum cofactor‑binding subunit |
| RA | 336,000 | G→A | A26T (GCG→ACG) | yahE → | DUF2877 domain‑containing protein YahE |
| RA | 340,464 | G→A | R100R (CGG→CGA) | yahI → | carbamate kinase‑like protein YahI |
| RA | 363,518 | A→G | Y930H (TAC→CAC) | lacZ ← | beta‑galactosidase |
| RA | 379,921 | (G)6→7 | intergenic (‑40/+148) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| JC | 380,020 | (G)10→7 | intergenic (‑139/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 380,022 | (G)10→11 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 436,757 | T→C | W57R (TGG→CGG) | pgpA → | phosphatidylglycerophosphatase A |
| RA | 486,305 | Δ1 bp | coding (545/648 nt) | acrR → | DNA‑binding transcriptional repressor AcrR |
| RA | 511,849 | T→C | V70A (GTC→GCC) | glsA → | glutaminase 1 |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 665,853 | A→G | V154A (GTG→GCG) | mrdB ← | SEDS family protein MrdB |
| RA | 704,616 | A→G | T225A (ACC→GCC) | nagE → | N‑acetylglucosamine specific PTS enzyme IIABC component |
| RA | 782,659 | A→G | D192G (GAC→GGC) | nadA → | quinolinate synthase |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 897,325 | T→C | I81T (ATC→ACC) | potI → | putrescine ABC transporter membrane subunit PotI |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 942,763 | A→G | E602G (GAA→GGA) | dmsA → | dimethyl sulfoxide reductase subunit A |
| RA | 960,067 | A→G | Q419R (CAG→CGG) | aroA → | 3‑phosphoshikimate 1‑carboxyvinyltransferase |
| RA | 977,782 | A→G | N486S (AAC→AGC) | mukB → | chromosome partitioning protein MukB |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,052,428 | C→T | G312D (GGC→GAC) | yccM ← | putative 4Fe‑4S membrane protein |
| RA | 1,093,922 | A→G | I349M (ATA→ATG) | dgcT → | putative diguanylate cyclase DgcT |
| RA | 1,138,175 | (G)5→6 | coding (805/942 nt) | flgJ → | putative peptidoglycan hydrolase FlgJ |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,159,060 | A→G | T398A (ACC→GCC) | ptsG → | glucose‑specific PTS enzyme IIBC component |
| RA | 1,190,712 | A→G | G425G (GGT→GGC) | purB ← | adenylosuccinate lyase |
| RA | 1,219,997 | A→G | pseudogene (397/2648 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 | 1,261,465 | A→G | G137G (GGT→GGC) | prs ← | ribose‑phosphate diphosphokinase |
| RA | 1,323,927 | T→C | R236R (CGT→CGC) | yciV → | RNA/ssDNA 5'‑>3' exonuclease |
| RA | 1,332,930 | A→G | E628G (GAG→GGG) | topA → | DNA topoisomerase 1 |
| RA | 1,432,217 | G→A | A1057T (GCT→ACT) | stfR → | Rac prophage; putative membrane protein |
| RA | 1,445,636 | A→G | A862A (GCA→GCG) | ydbH → | PF11739 family protein YdbH |
| RA | 1,465,997 | C→T | pseudogene (606/2518 nt) | ydbA → | putative outer membrane protein, N‑terminal fragment |
| RA | 1,466,533 | T→C | pseudogene (1142/2518 nt) | ydbA → | putative outer membrane protein, N‑terminal fragment |
| RA | 1,491,395 | A→G | N165S (AAC→AGC) | cybB → | cytochrome b561 |
| RA | 1,514,665 | (G)5→6 | coding (835/942 nt) | ydcU → | putative ABC transporter membrane subunit YdcU |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,550,453 | (G)5→6 | intergenic (+5/‑8) | fdnG → / → fdnH | formate dehydrogenase N subunit alpha/formate dehydrogenase N subunit beta |
| RA | 1,594,132 | (C)8→9 | pseudogene (3955/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,597,313 | (C)7→8 | pseudogene (774/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,610,001 | A→T | L227Q (CTG→CAG) | uxaB ← | tagaturonate reductase |
| RA | 1,634,642 | C→T | G82S (GGC→AGC) | tfaQ ← | Qin prophage; putative tail fiber assembly protein TfaQ |
| RA | 1,675,569 | G→A | N264N (AAC→AAT) | pntB ← | pyridine nucleotide transhydrogenase subunit beta |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,687,729 | G→A | R217C (CGC→TGC) | fumA ← | fumarase A |
| RA | 1,696,946 | G→A | A36V (GCC→GTC) | uidR ← | DNA‑binding transcriptional repressor UidR |
| RA | 1,727,494 | (G)6→8 | coding (836/1098 nt) | nemA → | N‑ethylmaleimide reductase |
| RA | 1,827,219 | T→C | E347E (GAA→GAG) | astB ← | N‑succinylarginine dihydrolase |
| RA | 1,853,128 | T→C | I284M (ATA→ATG) | ydjE ← | putative transporter YdjE |
| 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 | 1,901,630 | T→C | A51A (GCA→GCG) | yoaL ← | protein YoaL |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,013,820 | G→A | A198T (GCC→ACC) | fliF → | flagellar basal‑body MS‑ring and collar protein |
| RA | 2,054,066 | G→A | E142K (GAA→AAA) | shiA → | shikimate:H(+) symporter |
| RA | 2,102,842 | A→G | F24L (TTC→CTC) | insH‑7 ← | IS5 transposase and trans‑activator |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,185,875 | (G)7→8 | intergenic (‑79/‑42) | rcnR ← / → rcnA | DNA‑binding transcriptional repressor RcnR/Ni(2(+))/Co(2(+)) exporter |
| RA | 2,274,122 | T→C | W587R (TGG→CGG) | yejA → | putative oligopeptide ABC transporter periplasmic binding protein |
| RA | 2,278,738 | C→T | T341T (ACG→ACA) | bcr ← | multidrug efflux pump Bcr |
| RA | 2,288,526 | T→C | pseudogene (389/2525 nt) | yejO ← | adhesin‑like autotransporter YejO |
| RA | 2,288,561 | (C)7→8 | pseudogene (354/2525 nt) | yejO ← | adhesin‑like autotransporter YejO |
| RA | 2,296,418 | T→C | T203A (ACC→GCC) | ccmB ← | heme trafficking system membrane protein CcmB |
| RA | 2,300,856 | T→C | Y633C (TAC→TGC) | napA ← | periplasmic nitrate reductase subunit NapA |
| RA | 2,414,977 | T→C | G77G (GGT→GGC) | pta → | phosphate acetyltransferase |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,449,996 | T→C | E18E (GAA→GAG) | yfcO ← | DUF2544 domain‑containing protein YfcO |
| RA | 2,471,767 | (C)5→4 | pseudogene (296/519 nt) | yfdL ← | CPS‑53 (KpLE1) prophage; putative uncharacterized protein YfdL |
| RA | 2,500,102 | G→A | V478I (GTC→ATC) | ypdA → | sensory histidine kinase YpdA |
| RA | 2,511,625 | G→A | A361V (GCT→GTT) | mntH ← | Mn(2(+))/Fe(2(+)): H(+) symporter MntH |
| RA | 2,512,889 | T→C | intergenic (‑183/‑153) | mntH ← / → nupC | Mn(2(+))/Fe(2(+)): H(+) symporter MntH/nucleoside:H(+) symporter NupC |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,596,461 | T→C | T93A (ACC→GCC) | ypfJ ← | uncharacterized protein YpfJ |
| RA | 2,619,024 | G→A | G379G (GGC→GGT) | uraA ← | hypothetical protein |
| RA | 2,694,252 | T→C | N431S (AAC→AGC) | purL ← | phosphoribosylformylglycinamide synthetase |
| RA | 2,711,316 | T→C | H299H (CAT→CAC) | nadB → | L‑aspartate oxidase |
| RA | 2,712,093 | A→G | R224R (CGT→CGC) | yfiC ← | tRNA m(6)A37 methyltransferase |
| RA | 2,758,830 | T→C | L63L (TTA→CTA) | alpA → | CP4‑57 prophage; DNA‑binding transcriptional activator AlpA |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| RA | 2,817,885 | G→A | intergenic (‑25/+174) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,833,146 | C→T | A224V (GCC→GTC) | norV → | anaerobic nitric oxide reductase flavorubredoxin |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,865,733 | A→G | V211V (GTA→GTG) | ygbN → | putative transporter YgbN |
| RA | 2,873,038 | T→C | A100A (GCA→GCG) | ygbE ← | conserved inner membrane protein YgbE |
| RA | 2,908,002 | T→C | intergenic (‑61/+27) | eno ← / ← pyrG | enolase/CTP synthetase |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,993,230 | A→G | A379A (GCA→GCG) | ygeH → | putative transcriptional regulator YgeH |
| RA | 2,994,492 | T→C | pseudogene (412/444 nt) | ygeK ← | putative DNA‑binding transcriptional regulator YgeK |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,125,344 | T→C | Q39R (CAG→CGG) | glcF ← | glycolate dehydrogenase, putative iron‑sulfur subunit |
| RA | 3,183,190 | C→T | A214V (GCG→GTG) | zupT → | heavy metal divalent cation transporter ZupT |
| RA | 3,205,629 | T→C | N210D (AAC→GAC) | ttdR ← | DNA‑binding transcriptional activator Dan |
| RA | 3,223,947 | C→T | P439S (CCG→TCG) | ebgA → | evolved beta‑D‑galactosidase subunit alpha |
| RA | 3,236,458 | A→G | I167V (ATC→GTC) | ygjP → | putative metal‑dependent hydrolase |
| RA | 3,243,802 | G→A | P314S (CCG→TCG) | uxaC ← | D‑glucoronate/D‑galacturonate isomerase |
| RA | 3,246,318 | A→G | L365L (TTA→TTG) | exuT → | hexuronate transporter |
| RA | 3,256,262 | T→C | S130S (TCA→TCG) | cyuA ← | putative L‑cysteine desulfidase CyuA |
| RA | 3,294,906 | A→G | T503A (ACT→GCT) | lpoA → | outer membrane lipoprotein ‑ activator of MrcA activity |
| RA | 3,349,823 | G→A | L213L (CTG→TTG) | elbB ← | low activity glyoxalase ElbB |
| 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 | 3,419,006 | T→C | intergenic (+395/‑36) | yhdV → / → yhdW | lipoprotein YhdV/putative ABC transporter periplasmic binding protein YhdW |
| RA | 3,458,048 | T→C | S558P (TCA→CCA) | gspD → | Type II secretion system protein GspD |
| RA | 3,472,522 | A→G | G331G (GGT→GGC) | fusA ← | elongation factor G |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,650,680 | (C)7→6 | intergenic (+18/‑611) | arsC → / → yhiS | arsenate reductase/putative uncharacterized protein YhiS |
| RA | 3,650,746 | A→G | intergenic (+84/‑545) | arsC → / → yhiS | arsenate reductase/putative uncharacterized protein YhiS |
| RA | 3,664,969 | (T)8→7 | intergenic (+1/+17) | gadY → / ← gadX | small regulatory RNA GadY/DNA‑binding transcriptional dual regulator GadX |
| RA | 3,668,544 | (C)6→7 | coding (645/1398 nt) | ccp ← | cytochrome c peroxidase |
| RA | 3,805,159 | T→C | G264G (GGA→GGG) | 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 | 3,887,873 | T→C | V349A (GTG→GCG) | mnmE → | 5‑carboxymethylaminomethyluridine‑tRNA synthase GTPase subunit |
| RA | 3,948,631 | A→G | L447L (TTG→CTG) | yifB ← | putative magnesium chelatase YifB |
| RA | 4,013,361 | T→C | R103R (CGT→CGC) | metE → | cobalamin‑independent homocysteine transmethylase |
| RA | 4,062,912 | G→A | W222* (TGG→TGA) | yihN → | putative transporter YihN |
| RA | 4,087,770 | T→C | F257L (TTT→CTT) | yiiG → | DUF3829 domain‑containing lipoprotein YiiG |
| JC | 4,157,959 | Δ103 bp | coding (1110‑1212/1374 nt) | argH → | argininosuccinate lyase |
| RA | 4,277,878 | A→G | D137G (GAC→GGC) | soxR → | DNA‑binding transcriptional dual regulator SoxR |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,335,830 | G→A | A401V (GCC→GTC) | adiC ← | arginine:agmatine antiporter |
| RA | 4,342,094 | +G | coding (184/1356 nt) | melA → | alpha‑galactosidase |
| RA | 4,395,073 | (G)5→6 | coding (1008/1548 nt) | nnr → | NAD(P)HX epimerase/NAD(P)HX dehydratase |
| RA | 4,424,136 | T→C | V146A (GTG→GCG) | ulaF → | L‑ribulose‑5‑phosphate 4‑epimerase UlaF |
| RA | 4,432,592 | A→G | R155R (CGT→CGC) | ytfF ← | inner membrane protein YtfF |
| RA | 4,436,571 | A→G | intergenic (‑6/‑184) | cpdB ← / → cysQ | 2'3' cyclic nucleotide phosphodiesterase/3' nucleotidase/3'(2'),5'‑bisphosphate nucleotidase |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,459,063 | A→G | T369A (ACC→GCC) | pmbA → | metalloprotease PmbA |
| RA | 4,621,090 | T→C | C70R (TGC→CGC) | deoD → | purine nucleoside phosphorylase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423777–3424233 | 3424525–3424238 | 6–749 | 15 [13] | [12] 15 | [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) | 52 (1.320) | 15/188 | 1.3 | 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) | 45 (1.140) | 21/188 | 0.7 | 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 | = 375064 | NA (NA) | 21 (0.530) | 16/190 | 1.2 | NA | noncoding (33/34 nt) | other | REP31c |
| ? | NC_000913 | = 377487 | NA (NA) | intergenic (+176/+48) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 375102 = | NA (NA) | 46 (1.030) | 25/214 | 0.6 | NA | noncoding (17/36 nt) | other | REP31d |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 375203 = | NA (NA) | 42 (0.940) | 26/214 | 0.6 | NA | noncoding (17/36 nt) | other | REP31f |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 1207790 = | 6 (0.100) | 85 (1.680) | 51/242 | 0.0 | 91.7% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 10 (0.200) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 5 (0.090) | 36 (0.710) | 30/242 | 0.5 | 83.3% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 10 (0.200) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 42 (0.750) | 36/266 | 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 = | 77 (1.340) | 81 (1.420) | 55/272 | 0.1 | 67.9% | 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) | 62 (1.080) | 42/274 | 0.3 | 96.9% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 2 (0.030) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||