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 | 31,834 | A→G | T340A (ACT→GCT) | carB → | carbamoyl phosphate synthetase subunit beta |
| RA | 34,120 | (T)9→8 | intergenic (+82/‑180) | carB → / → caiF | carbamoyl phosphate synthetase subunit beta/DNA‑binding transcriptional activator CaiF |
| RA | 35,374 | T→C | intergenic (‑3/+3) | caiE ← / ← caiD | putative transferase CaiE/crotonobetainyl‑CoA hydratase |
| RA | 38,488 | A→G | Y210H (TAC→CAC) | caiB ← | gamma‑butyrobetainyl‑CoA:carnitine CoA transferase |
| RA | 51,147 | T→C | T26A (ACC→GCC) | apaH ← | diadenosine tetraphosphatase |
| RA | 117,350 | T→C | D67G (GAC→GGC) | ppdD ← | prepilin peptidase‑dependent protein |
| RA | 163,298 | A→G | A398A (GCA→GCG) | hrpB → | putative ATP‑dependent RNA helicase HrpB |
| RA | 173,121 | A→G | T554A (ACC→GCC) | fhuB → | iron(III) hydroxamate ABC transporter membrane subunit |
| RA | 196,868 | A→G | N108S (AAC→AGC) | rseP → | intramembrane zinc metalloprotease |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 355,356 | (T)6→7 | coding (435/1260 nt) | codB → | cytosine transporter |
| RA | 373,839 | T→C | S307P (TCA→CCA) | mhpF → | acetaldehyde dehydrogenase (acylating) |
| RA | 376,578 | G→A | A374T (GCC→ACC) | mhpT → | 3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| RA | 380,022 | (G)10→9 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 732,070 | C→T | R830C (CGT→TGT) | rhsC → | rhs element protein RhsC |
| RA | 845,317 | A→G | V55A (GTG→GCG) | ybiO ← | moderate conductance mechanosensitive channel |
| RA | 845,350 | (T)8→7 | coding (131/2226 nt) | ybiO ← | moderate conductance mechanosensitive channel |
| RA | 852,372 | A→G | F76L (TTC→CTC) | opgE ← | phosphoethanolamine transferase |
| RA | 868,422 | (C)8→7 | coding (903/1872 nt) | gsiA → | glutathione ABC transporter ATP binding subunit GsiA |
| RA | 872,365 | T→C | V159A (GTG→GCG) | gsiD → | glutathione ABC transporter membrane subunit GsiD |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 928,883 | G→A | P105S (CCC→TCC) | cydC ← | glutathione/L‑cysteine ABC exporter subunit CydC |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 969,637 | A→G | E83E (GAA→GAG) | ycaQ → | winged helix DNA‑binding domain‑containing protein YcaQ |
| RA | 994,795 | (G)5→6 | coding (38/792 nt) | ssuC ← | aliphatic sulfonate ABC transporter membrane subunit |
| RA | 1,002,901 | (A)7→6 | coding (13/543 nt) | ycbU → | putative fimbrial protein YcbU |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,052,945 | A→G | F140L (TTT→CTT) | yccM ← | putative 4Fe‑4S membrane protein |
| RA | 1,098,387 | A→G | T168A (ACC→GCC) | ghrA → | glyoxylate/hydroxypyruvate reductase A |
| RA | 1,114,595 | A→G | V299A (GTA→GCA) | mdtG ← | efflux pump MdtG |
| RA | 1,140,047 | A→C | T5T (ACA→ACC) | flgL → | flagellar hook‑filament junction protein 2 |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,148,066 | C→T | A149V (GCC→GTC) | plsX → | putative phosphate acyltransferase |
| RA | 1,157,796 | A→G | intergenic (+222/‑73) | ycfH → / → ptsG | putative metal‑dependent hydrolase YcfH/glucose‑specific PTS enzyme IIBC component |
| RA | 1,170,674 | C→T | P1097P (CCG→CCA) | mfd ← | transcription‑repair coupling factor |
| RA | 1,174,377 | A→G | G263G (GGT→GGC) | ycfT ← | inner membrane protein YcfT |
| RA | 1,182,826 | (T)6→5 | coding (4/1047 nt) coding (795/795 nt) |
potD ← potC ← |
spermidine preferential ABC transporter periplasmic binding protein spermidine preferential ABC transporter membrane subunit PotC |
| RA | 1,189,703 | A→G | V25A (GTA→GCA) | phoQ ← | sensory histidine kinase PhoQ |
| RA | 1,219,636 | A→G | pseudogene (36/2648 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 | 1,235,642 | C→T | A235A (GCC→GCT) | fadR → | DNA‑binding transcriptional dual regulator FadR |
| RA | 1,265,726 | A→G | T239A (ACC→GCC) | prfA → | peptide chain release factor RF1 |
| RA | 1,275,320 | A→G | G170G (GGT→GGC) | narL ← | DNA‑binding transcriptional dual regulator NarL |
| RA | 1,408,047 | A→G | intergenic (‑252/‑3) | dgcM ← / → zntB | diguanylate cyclase DgcM/Zn(2(+)):H(+) symporter |
| RA | 1,428,884 | A→G | pseudogene (89/189 nt) | lomR → | Rac prophage; protein LomR_1 |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,553,360 | C→T | R160H (CGT→CAT) | adhP ← | ethanol dehydrogenase/alcohol dehydrogenase |
| RA | 1,635,505 | T→C | T115A (ACT→GCT) | ydfN ← | Qin prophage; putative side tail fiber assembly protein |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,700,737 | T→C | G461G (GGT→GGC) | malX → | PTS enzyme IIBC component MalX |
| RA | 1,704,195 | A→G | S38S (AGT→AGC) | ydgJ ← | putative oxidoreductase YdgJ |
| RA | 1,796,602 | G→A | A448V (GCG→GTG) | pheT ← | phenylalanine‑‑tRNA ligase subunit beta |
| RA | 1,816,368 | T→C | intergenic (+240/+18) | katE → / ← chbG | catalase II/chitin disaccharide deacetylase |
| RA | 1,821,867 | (A)8→9 | intergenic (‑248/+51) | chbB ← / ← osmE | N,N'‑diacetylchitobiose‑specific PTS enzyme IIB component/osmotically‑inducible lipoprotein OsmE |
| 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 |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,002,150 | T→C | N486S (AAC→AGC) | fliC ← | flagellar filament structural protein |
| RA | 2,016,617 | T→C | L22L (TTG→CTG) | fliI → | flagellum‑specific ATP synthase FliI |
| RA | 2,028,703 | A→G | L222L (TTG→CTG) | yedI ← | conserved inner membrane protein YedI |
| RA | 2,070,960 | A→G | pseudogene (175/426 nt) | yeeP → | CP4‑44 prophage; putative GTP‑binding protein |
| RA | 2,095,429 | G→A | G102D (GGC→GAC) | hisA → | 1‑(5‑phosphoribosyl)‑5‑[(5‑ phosphoribosylamino)methylideneamino]imidazole‑4‑ carboxamide isomerase |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,205,964 | A→G | A90A (GCA→GCG) | yehM → | putative YehN |
| RA | 2,260,261 | G→A | Q384* (CAG→TAG) | fruA ← | fructose‑specific PTS multiphosphoryl transfer protein FruA |
| RA | 2,277,598 | T→C | R433R (CGT→CGC) | yejF → | putative oligopeptide ABC transporter ATP binding subunit |
| RA | 2,345,426 | A→G | T188A (ACG→GCG) | nrdA → | ribonucleoside‑diphosphate reductase 1 subunit alpha |
| RA | 2,419,382 | (C)6→7 | coding (407/555 nt) | yfcE ← | phosphodiesterase YfcE |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,462,889 | (C)9→8 | intergenic (+243/‑123) | fadL → / → yfdF | long‑chain fatty acid outer membrane channel/bacteriophage T2 receptor/protein YfdF |
| RA | 2,493,615 | T→C | intergenic (‑361/+152) | frc ← / ← yfdX | formyl‑CoA transferase/protein YfdX |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,599,314 | G→A | G149G (GGC→GGT) | dapA ← | 4‑hydroxy‑tetrahydrodipicolinate synthase |
| RA | 2,737,713 | (G)6→5 | intergenic (+67/‑32) | pheL → / → pheA | phe operon leader peptide/fused chorismate mutase/prephenate dehydratase |
| RA | 2,746,038 | T→C | T50A (ACT→GCT) | rpsP ← | 30S ribosomal subunit protein S16 |
| RA | 2,759,005 | C→T | F7F (TTC→TTT) | yfjI → | CP4‑57 prophage; protein YfjI |
| RA | 2,779,929 | T→C | N933S (AAC→AGC) | ypjA ← | adhesin‑like autotransporter YpjA |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| RA | 2,835,958 | G→A | P490S (CCG→TCG) | hypF ← | carbamoyltransferase HypF |
| RA | 2,839,743 | G→A | A74T (GCC→ACC) | ascF → | beta‑glucoside specific PTS enzyme IIBC component |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,901,288 | G→A | V233I (GTC→ATC) | yqcE → | putative transport protein YqcE |
| RA | 2,933,495 | T→C | E65G (GAG→GGG) | fucA ← | L‑fuculose‑phosphate aldolase |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 3,060,772 | (T)8→9 | intergenic (+126/‑78) | argP → / → scpA | DNA‑binding transcriptional dual regulator ArgP/methylmalonyl‑CoA mutase |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,101,039 | (C)7→8 | coding (585/720 nt) | yggN ← | putative EcfF |
| RA | 3,168,793 | T→C | T147A (ACA→GCA) | ygiV ← | DNA‑binding transcriptional repressor YgiV |
| RA | 3,245,580 | T→C | G119G (GGT→GGC) | exuT → | hexuronate transporter |
| RA | 3,265,334 | C→T | G232D (GGC→GAC) | tdcB ← | catabolic threonine dehydratase |
| RA | 3,344,248 | T→C | V102A (GTA→GCA) | lptB → | lipopolysaccharide transport system ATP binding protein |
| 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 | 3,467,721 | T→C | E711E (GAA→GAG) | chiA ← | endochitinase |
| RA | 3,555,899 | C→T | E317E (GAG→GAA) | rtcA ← | RNA 3'‑terminal phosphate cyclase |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,735,053 | C→T | G25G (GGC→GGT) | xylR → | DNA‑binding transcriptional dual regulator XylR |
| RA | 3,781,031 | (C)5→4 | intergenic (+14/‑184) | lldD → / → trmL | L‑lactate dehydrogenase/tRNA (cytidine/uridine‑2'‑O)‑ribose methyltransferase |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,836,534 | (C)6→5 | intergenic (+218/‑419) | selC → / → setC | tRNA‑Sec/putative arabinose exporter |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 3,897,560 | C→T | P19S (CCG→TCG) | cbrB → | putative inner membrane protein |
| RA | 4,015,840 | A→G | G110G (GGT→GGC) | ysgA ← | putative dienelactone hydrolase |
| RA | 4,028,917 | A→G | D685D (GAT→GAC) | fadB ← | dodecenoyl‑CoA delta‑isomerase, enoyl‑CoA hydratase, 3‑hydroxybutyryl‑CoA epimerase, 3‑hydroxyacyl‑CoA dehydrogenase |
| RA | 4,057,062 | G→A | P325S (CCG→TCG) | glnA ← | glutamine synthetase |
| RA | 4,265,990 | (G)6→7 | coding (209/1080 nt) | alr → | alanine racemase 1 |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,390,182 | T→C | Y60C (TAC→TGC) | psd ← | phosphatidylserine decarboxylase proenzyme |
| RA | 4,397,446 | A→G | N12S (AAC→AGC) | mutL → | DNA mismatch repair protein MutL |
| RA | 4,426,393 | A→G | T96A (ACT→GCT) | rplI → | 50S ribosomal subunit protein L9 |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,572,093 | (T)6→7 | intergenic (+178/‑321) | yjiS → / → yjiT | DUF1127 domain‑containing protein YjiS/putative uncharacterized protein YjiT |
| RA | 4,586,671 | C→T | D31N (GAT→AAT) | hsdR ← | type I restriction enzyme EcoKI endonuclease component |
| RA | 4,606,215 | (G)8→9 | noncoding (72/87 nt) | leuP ← | tRNA‑Leu |
| RA | 4,634,054 | T→C | G86G (GGT→GGC) | ytjC → | putative phosphatase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1632695–1632732 | 1635496 | 2765–2802 | 21 [19] | [18] 20 | ynfT–[ydfN] | ynfT,ydfK,pinQ,tfaQ,[ydfN] |
| * | * | ÷ | NC_000913 | 3423766–3424233 | 3424526–3424240 | 8–761 | 21 [19] | [18] 20 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 10 (0.140) | 89 (1.430) | 55/244 | 0.1 | 90.9% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 9 (0.140) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 10 (0.140) | 49 (0.790) | 42/244 | 0.3 | 84.6% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 9 (0.140) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 85 (1.240) | 61/268 | 0.1 | 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 = | 107 (1.510) | 116 (1.650) | 63/274 | 0.0 | 68.4% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 1 (0.010) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 83 (1.170) | 51/276 | 0.2 | 97.7% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 2 (0.030) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | 4542682 = | 57 (0.810) | 20 (0.300) | 18/258 | 2.3 | 29.1% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 44 (0.670) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||