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 | 190,530 | A→G | A219A (GCA→GCG) | rpsB → | 30S ribosomal subunit protein S2 |
| RA | 218,588 | T→G | N63T (AAC→ACC) | proS ← | proline‑‑tRNA ligase |
| RA | 241,205 | A→G | V700A (GTG→GCG) | fadE ← | acyl‑CoA dehydrogenase |
| RA | 243,023 | C→T | G94D (GGC→GAC) | fadE ← | acyl‑CoA dehydrogenase |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 332,811 | A→G | E147E (GAA→GAG) | pdeL → | DNA‑binding transcriptional activator/c‑di‑GMP phosphodiesterase PdeL |
| MC JC | 338,740 | Δ11 bp | coding (416‑426/1419 nt) | yahG → | DUF1116 domain‑containing protein YahG |
| RA | 380,021 | (G)10→8 | intergenic (‑140/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 412,685 | A→G | R1023R (CGT→CGC) | sbcC ← | ATP dependent, structure specific DNA nuclease ‑ SbcC subunit |
| RA | 423,467 | A→G | D317G (GAC→GGC) | malZ → | maltodextrin glucosidase |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 532,918 | A→G | E156E (GAA→GAG) | allA → | ureidoglycolate lyase |
| RA | 637,395 | T→C | H75R (CAC→CGC) | ybdO ← | putative LysR family DNA‑binding transcriptional regulator YbdO |
| RA | 706,847 | T→C | V252A (GTT→GCT) | glnS → | glutamine‑‑tRNA ligase |
| RA | 777,361 | T→C | Y340Y (TAT→TAC) | tolA → | Tol‑Pal system protein TolA |
| RA | 853,778 | C→T | T44T (ACC→ACT) | ybiR → | putative transporter YbiR |
| 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 | 945,505 | A→G | V18A (GTT→GCT) | ycaC ← | putative hydrolase |
| RA | 1,007,942 | T→C | G33G (GGT→GGC) | rlmL → | fused 23S rRNA m(2)G2445 methyltransferase and 23S rRNA m(7)G2069 methyltransferase |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,023,670 | A→G | F72L (TTC→CTC) | yccS ← | putative transporter YccS |
| RA | 1,043,947 | T→C | A88A (GCA→GCG) | etk ← | protein‑tyrosine kinase Etk |
| RA | 1,063,627 | G→A | A50V (GCT→GTT) | cbpA ← | curved DNA‑binding protein |
| RA | 1,130,841 | A→G | V8A (GTG→GCG) | flgA ← | flagellar basal body P‑ring formation protein FlgA |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,210,492 | A→G | E49E (GAA→GAG) | mcrA → | e14 prophage; 5‑methylcytosine‑specific restriction enzyme McrA |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,263,889 | T→C | V59A (GTT→GCT) | hemA → | glutamyl‑tRNA reductase |
| RA | 1,388,876 | A→G | intergenic (‑65/‑54) | tpx ← / → ycjG | lipid hydroperoxide peroxidase/L‑Ala‑D/L‑Glu epimerase |
| RA | 1,532,043 | A→G | R76R (AGA→AGG) | ydcC → | H repeat‑associated putative transposase YdcC |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,547,856 | C→A | G152G (GGC→GGA) | fdnG → | formate dehydrogenase N subunit alpha |
| RA | 1,634,642 | C→T | G82S (GGC→AGC) | tfaQ ← | Qin prophage; putative tail fiber assembly protein TfaQ |
| RA | 1,645,530 | T→C | E35G (GAG→GGG) | relE ← | Qin prophage; mRNA interferase toxin RelE |
| RA | 1,650,640 | T→C | pseudogene (563/921 nt) | ydfE → | Qin prophage; protein YdfE |
| RA | 1,679,505 | C→T | intergenic (+134/‑52) | ydgH → / → ydgI | DUF1471 domain‑containing protein YdgH/putative arginine:ornithine antiporter |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,691,588 | A→G | *422Q (TAA→CAA) | uidC ← | outer membrane porin family protein |
| RA | 1,696,365 | (G)6→7 | intergenic (‑294/+97) | uidA ← / ← uidR | beta‑glucuronidase/DNA‑binding transcriptional repressor UidR |
| RA | 1,790,331 | A→G | V305A (GTT→GCT) | ydiU ← | UPF0061 family protein YdiU |
| RA | 1,804,371 | T→C | pseudogene (1278/1900 nt) | arpB → | putative ankyrin repeat protein B, N‑terminal fragment |
| RA | 1,812,949 | A→G | S62P (TCT→CCT) | ydjO ← | protein YdjO |
| RA | 1,844,343 | T→C | S177G (AGC→GGC) | ynjI ← | DUF1266 domain‑containing protein YnjI |
| 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 | 2,012,563 | (G)6→7 | pseudogene (62/279 nt) | intG → | putative defective phage integrase |
| RA | 2,034,899 | T→C | pseudogene (849/1193 nt) | yedS → | putative outer membrane protein YedS, N‑terminal fragment |
| RA | 2,048,871 | A→G | K1312E (AAG→GAG) | yeeJ → | inverse autotransporter adhesin |
| RA | 2,124,459 | G→A | P21L (CCG→CTG) | cpsB ← | mannose‑1‑phosphate guanylyltransferase |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,191,135 | G→A | R171C (CGC→TGC) | yehC ← | putative fimbrial chaperone YehC |
| RA | 2,198,746 | T→C | intergenic (+1448/‑1533) | yehF → / → yehI | putative protein YehF/DUF4132 domain‑containing protein YehI |
| RA | 2,261,917 | A→G | F150S (TTC→TCC) | fruK ← | 1‑phosphofructokinase |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,455,256 | T→C | T131A (ACC→GCC) | yfcV ← | putative fimbrial protein YfcV |
| RA | 2,459,911 | T→C | T187A (ACC→GCC) | fadI ← | 3‑ketoacyl‑CoA thiolase FadI |
| RA | 2,462,889 | (C)9→10 | intergenic (+243/‑123) | fadL → / → yfdF | long‑chain fatty acid outer membrane channel/bacteriophage T2 receptor/protein YfdF |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,604,871 | T→C | F21L (TTT→CTT) | hyfD → | hydrogenase 4 component D |
| RA | 2,634,366 | T→C | G45G (GGT→GGC) | xseA → | exodeoxyribonuclease VII subunit XseA |
| RA | 2,637,605 | T→C | N350D (AAC→GAC) | bamB ← | outer membrane protein assembly factor BamB |
| RA | 2,670,206 | T→C | L392P (CTG→CCG) | hcaE → | putative 3‑phenylpropionate/cinnamate dioxygenase subunit alpha |
| RA | 2,680,354 | C→T | A798T (GCC→ACC) | yphG ← | DUF5107 domain‑containing protein YphG |
| RA | 2,701,212 | G→A | A173V (GCG→GTG) | pdxJ ← | pyridoxine 5'‑phosphate synthase |
| RA | 2,771,295 | A→G | T50A (ACC→GCC) | yfjT → | CP4‑57 prophage; uncharacterized protein YfjT |
| RA | 2,800,337 | T→C | R64R (CGT→CGC) | ygaM → | DUF883 domain‑containing protein YgaM |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| RA | 2,848,921 | G→A | N107N (AAC→AAT) | hycC ← | formate hydrogenlyase subunit HycC |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,863,781 | A→G | K63K (AAA→AAG) | ygbL → | putative 3‑oxo‑tetronate 4‑phosphate decarboxylase YgbL |
| RA | 2,891,771 | A→G | V43A (GTA→GCA) | cysJ ← | sulfite reductase, flavoprotein subunit |
| RA | 2,930,705 | T→C | L377P (CTC→CCC) | sdaB → | L‑serine deaminase II |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 3,003,479 | (G)6→7 | coding (866/879 nt) | xdhB → | putative xanthine dehydrogenase FAD‑binding subunit XdhB |
| RA | 3,054,650 | A→G | V64A (GTG→GCG) | pepP ← | proline aminopeptidase P II |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,090,950 | T→C | Y202H (TAT→CAT) | endA → | DNA‑specific endonuclease I |
| RA | 3,096,185 | Δ1 bp | coding (366/567 nt) | yggT → | uncharacterized protein YggT |
| RA | 3,104,118 | T→C | F9S (TTC→TCC) | yggX → | putative Fe(2(+))‑trafficking protein |
| RA | 3,110,037 | T→C | I162T (ATC→ACC) | yqgA → | DUF554 domain‑containing protein YqgA |
| RA | 3,177,926 | A→G | intergenic (‑16/‑189) | nudF ← / → tolC | ADP‑sugar pyrophosphatase/outer membrane channel TolC |
| RA | 3,268,574 | A→G | N54D (AAC→GAC) | yhaC → | uncharacterized protein YhaC |
| RA | 3,273,214 | T→C | Y115C (TAC→TGC) | garL ← | alpha‑dehydro‑beta‑deoxy‑D‑glucarate aldolase |
| RA | 3,306,971 | T→C | D297G (GAC→GGC) | deaD ← | ATP‑dependent RNA helicase DeaD |
| RA | 3,347,113 | A→G | intergenic (+44/‑2) | ptsN → / → rapZ | phosphotransferase system enzyme IIA(Ntr)/RNase adaptor protein |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,374,987 | T→C | V40A (GTC→GCC) | dcuD → | putative transporter DcuD |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,436,634 | A→G | L39L (TTA→TTG) | trkA → | NAD‑binding component of Trk potassium transporters |
| RA | 3,519,690 | C→T | V338V (GTG→GTA) | hofQ ← | DNA utilization protein HofQ |
| RA | 3,542,997 | T→C | intergenic (+33/‑170) | feoC → / → rpnA | ferrous iron transport protein FeoC/recombination‑promoting nuclease RpnA |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,622,670 | C→A | T1160K (ACG→AAG) | rhsB → | rhs element protein RhsB |
| RA | 3,622,678 | G→A | A1163T (GCA→ACA) | rhsB → | rhs element protein RhsB |
| RA | 3,622,761 | G→C | R1190R (CGG→CGC) | rhsB → | rhs element protein RhsB |
| RA | 3,622,839 | A→G | R1216R (CGA→CGG) | rhsB → | rhs element protein RhsB |
| RA | 3,649,339 | T→C | T135T (ACT→ACC) | arsB → | arsenite/antimonite:H(+) antiporter |
| RA | 3,791,751 | A→G | R267R (CGT→CGC) | kbl ← | 2‑amino‑3‑ketobutyrate CoA ligase |
| 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 | 3,885,620 | A→G | N182S (AAC→AGC) | yidC → | membrane protein insertase YidC |
| RA | 3,887,189 | T→C | L121P (CTT→CCT) | mnmE → | 5‑carboxymethylaminomethyluridine‑tRNA synthase GTPase subunit |
| RA | 3,902,375 | T→C | T443A (ACA→GCA) | bglB ← | 6‑phospho‑beta‑glucosidase B |
| RA | 4,013,566 | A→G | K172E (AAA→GAA) | metE → | cobalamin‑independent homocysteine transmethylase |
| RA | 4,101,728 | (G)7→8 | coding (39/984 nt) | kdgT → | 2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| RA | 4,197,163 | A→G | Q87Q (CAA→CAG) | nudC → | NADH pyrophosphatase |
| RA | 4,204,874 | C→T | G353D (GGC→GAC) | purD ← | phosphoribosylamine‑‑glycine ligase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,331,722 | G→A | A407A (GCG→GCA) | proP → | osmolyte:H(+) symporter ProP |
| RA | 4,335,130 | A→G | V154A (GTT→GCT) | eptA ← | phosphoethanolamine transferase EptA |
| RA | 4,378,361 | A→G | F195S (TTC→TCC) | ampC ← | beta‑lactamase |
| RA | 4,436,450 | A→G | F39S (TTC→TCC) | cpdB ← | 2'3' cyclic nucleotide phosphodiesterase/3' nucleotidase |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,497,835 | A→G | pseudogene (1086/1191 nt) | intB → | KpLE2 phage‑like element; putative integrase |
| RA | 4,595,493 | C→T | G120D (GGT→GAT) | lgoR ← | putative DNA‑binding transcriptional regulator LgoR |
| RA | 4,640,455 | C→T | N18N (AAC→AAT) | yjjY → | protein YjjY |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1097055–1097108 | 1097495–1097172 | 65–441 | 7 [5] | [5] 6 | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | * | ÷ | NC_000913 | 1432740–1433196 | 1433976–1433671 | 476–1237 | 6 [5] | [5] 6 | [tfaR]–pinR | [tfaR],pinR |
| * | * | ÷ | NC_000913 | 3423770–3424234 | 3424523–3424239 | 6–754 | 6 [4] | [4] 6 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3619386–3620321 | 3622204–3621189 | 869–2819 | 6 [5] | [5] 6 | rhsB | rhs element protein RhsB |
| * | * | ÷ | NC_000913 | 3762391–3763312 | 3765183–3764180 | 869–2793 | 6 [4] | [5] 6 | rhsA | rhs element protein RhsA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 374922 = | NA (NA) | 6 (0.250) | 4/202 | 2.5 | NA | intergenic (+41/‑537) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377430 = | NA (NA) | intergenic (+119/+105) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 1207790 = | 6 (0.190) | 55 (1.930) | 43/244 | 0.0 | 87.1% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 11 (0.390) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 6 (0.190) | 21 (0.740) | 18/244 | 0.5 | 72.0% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 11 (0.390) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 35 (1.120) | 26/268 | 0.2 | 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 = | 40 (1.240) | 43 (1.340) | 33/274 | 0.1 | 67.9% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 1 (0.030) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 42 (1.300) | 33/276 | 0.1 | 97.7% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 1 (0.030) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||