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 | 1,152 | (C)5→6 | coding (816/2463 nt) | thrA → | fused aspartate kinase/homoserine dehydrogenase 1 |
| RA | 70,787 | T→C | F134S (TTT→TCT) | araC → | DNA‑binding transcriptional dual regulator AraC |
| RA | 81,547 | Δ2 bp | coding (411‑412/1092 nt) | leuB ← | 3‑isopropylmalate dehydrogenase |
| RA | 84,997 | A→G | Q210Q (CAA→CAG) | leuO → | DNA‑binding transcriptional dual regulator LeuO |
| RA | 92,651 | C→T | A413A (GCC→GCT) | ftsI → | peptidoglycan DD‑transpeptidase FtsI |
| RA | 175,792 | A→G | Y229C (TAC→TGC) | clcA → | chloride:H(+) antiporter ClcA |
| RA | 176,294 | A→G | A396A (GCA→GCG) | clcA → | chloride:H(+) antiporter ClcA |
| RA | 192,206 | A→G | S118G (AGC→GGC) | pyrH → | UMP kinase |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 279,853 | C→T | C8Y (TGT→TAT) | insA‑2 ← | IS1 protein InsA |
| RA | 285,647 | (G)6→7 | coding (253/1383 nt) | yagG → | putative D‑xylonate transporter YagG |
| RA | 286,748 | C→T | P452S (CCC→TCC) | yagG → | putative D‑xylonate transporter YagG |
| RA | 298,590 | A→G | L46P (CTG→CCG) | paoD ← | molybdenum cofactor insertion chaperone for PaoABC |
| RA | 344,068 | T→C | intergenic (+135/‑108) | yahK → / → yahL | aldehyde reductase, NADPH‑dependent/uncharacterized protein YahL |
| RA | 366,261 | A→G | R15R (CGT→CGC) | lacZ ← | beta‑galactosidase |
| RA | 375,168 | G→A | intergenic (+287/‑291) | mhpE → / → mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| RA | 375,176 | A→G | intergenic (+295/‑283) | mhpE → / → mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| RA | 411,118 | A→G | intergenic (+66/+179) | mak → / ← araJ | manno(fructo)kinase/putative transport protein AraJ |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 795,107 | A→G | N7D (AAC→GAC) | modA → | molybdate ABC transporter periplasmic binding protein |
| RA | 828,529 | A→G | C151C (TGT→TGC) | ybhF ← | putative ABC exporter ATP binding subunit |
| RA | 846,384 | C→T | G27D (GGC→GAC) | glnQ ← | L‑glutamine ABC transporter ATP binding subunit |
| RA | 871,184 | T→C | V73A (GTG→GCG) | gsiC → | glutathione ABC transporter membrane subunit GsiC |
| 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 | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,103,590 | A→G | intergenic (‑394/‑361) | csgD ← / → csgB | DNA‑binding transcriptional dual regulator CsgD/curlin, minor subunit |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,205,003 | A→G | V278V (GTA→GTG) pseudogene (603/1137 nt) |
ymfN → aaaE → |
e14 prophage; chimeric replication protein/phage terminase YmfN phage terminase |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,298,954 | T→C | G119G (GGT→GGC) | ychE → | putative inner membrane protein |
| RA | 1,319,424 | T→C | Y122C (TAC→TGC) | trpC ← | fused indole‑3‑glycerol phosphate synthase/phosphoribosylanthranilate isomerase |
| RA | 1,351,196 | (G)7→8 | intergenic (‑157/+211) | fabI ← / ← ycjD | enoyl‑[acyl‑carrier‑protein] reductase/DUF559 domain‑containing protein YcjD |
| RA | 1,370,293 | A→G | V26V (GTA→GTG) | ycjM → | glucosylglycerate phosphorylase |
| RA | 1,398,613 | A→G | Y4H (TAT→CAT) | uspE ← | universal stress protein with a role cellular motility |
| RA | 1,454,645 | T→C | V240A (GTT→GCT) | paaA → | phenylacetyl‑CoA 1,2‑epoxidase, monooxygenase subunit |
| RA | 1,457,034 | C→T | A202V (GCC→GTC) | paaE → | phenylacetyl‑CoA 1,2‑epoxidase, reductase subunit |
| RA | 1,522,527 | C→T | G180E (GGG→GAG) | yncD ← | putative TonB‑dependent outer membrane receptor |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,588,397 | G→A | P148L (CCT→CTT) | ydeS ← | putative fimbrial protein YdeS |
| RA | 1,626,876 | T→C | T169A (ACC→GCC) | dcp ← | peptidyl‑dipeptidase Dcp |
| RA | 1,634,642 | C→T | G82S (GGC→AGC) | tfaQ ← | Qin prophage; putative tail fiber assembly protein TfaQ |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,717,473 | C→A | G179C (GGC→TGC) | pdxH ← | pyridoxal 5‑phosphate synthase |
| RA | 1,721,103 | T→C | F27L (TTC→CTC) | ydhI → | DUF1656 domain‑containing protein YdhI |
| RA | 1,760,000 | T→C | N175S (AAC→AGC) | sufS ← | L‑cysteine desulfurase |
| RA | 1,769,478 | (G)7→8 | coding (405/1113 nt) | ydiK → | putative transporter YdiK |
| RA | 1,785,430 | T→C | E561E (GAA→GAG) | ppsA ← | phosphoenolpyruvate synthetase |
| RA | 1,827,696 | T→C | E188E (GAA→GAG) | astB ← | N‑succinylarginine dihydrolase |
| RA | 1,838,231 | (G)5→4 | coding (1020/1536 nt) | ynjC → | putative ABC transporter membrane subunit YnjC |
| 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 | 1,934,907 | T→C | T470A (ACC→GCC) | zwf ← | NADP(+)‑dependent glucose‑6‑phosphate dehydrogenase |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 1,996,183 | T→C | N217S (AAC→AGC) | sdiA ← | DNA‑binding transcriptional dual regulator SdiA |
| RA | 2,038,337 | C→T | A163T (GCT→ACT) | hprR ← | DNA‑binding transcriptional dual regulator HprR |
| RA | 2,060,085 | C→T | G277E (GGA→GAA) | cbl ← | DNA‑binding transcriptional activator Cbl |
| RA | 2,168,392 | A→G | intergenic (‑86/‑320) | yegR ← / → yegS | uncharacterized protein YegR/lipid kinase |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,235,592 | G→A | G110R (GGG→AGG) | preA → | NAD‑dependent dihydropyrimidine dehydrogenase subunit PreA |
| RA | 2,251,690 | T→C | V284A (GTA→GCA) | nfo → | endonuclease IV |
| RA | 2,421,048 | T→C | V143A (GTA→GCA) | yfcG → | disulfide reductase |
| RA | 2,441,842 | G→A | V27I (GTC→ATC) | mnmC → | fused 5‑methylaminomethyl‑2‑thiouridine‑forming methyltransferase and FAD‑dependent demodification enzyme |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,555,207 | A→G | intergenic (‑25/+21) | eutR ← / ← eutK | putative AraC‑type transcriptional regulator EutR/putative structural protein, ethanolamine utilization microcompartment |
| RA | 2,795,996 | C→T | A108V (GCG→GTG) | csiR → | DNA‑binding transcriptional repressor CsiR |
| RA | 2,800,662 | A→G | intergenic (+187/‑61) | ygaM → / → nrdH | DUF883 domain‑containing protein YgaM/glutaredoxin‑like protein |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| RA | 2,816,829 | T→C | S38G (AGT→GGT) | yqaA ← | DedA family protein YqaA |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,867,181 | T→C | N124S (AAC→AGC) | rpoS ← | RNA polymerase, sigma S (sigma 38) factor |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,977,802 | T→C | A366A (GCA→GCG) | lysA ← | diaminopimelate decarboxylase |
| RA | 3,008,069 | T→C | V187A (GTA→GCA) | ygeX → | 2,3‑diaminopropionate ammonia‑lyase |
| RA | 3,045,986 | Δ1 bp | intergenic (‑85/+182) | ygfF ← / ← gcvP | putative NAD(P)‑binding oxidoreductase with NAD(P)‑binding Rossmann‑fold domain/glycine decarboxylase |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,128,145 | (T)8→7 | intergenic (‑124/‑127) | glcD ← / → glcC | glycolate dehydrogenase, putative FAD‑linked subunit/DNA‑binding transcriptional dual regulator GlcC |
| RA | 3,201,043 | T→C | intergenic (‑78/‑164) | ygiF ← / → ygiM | inorganic triphosphatase/putative signal transduction protein (SH3 domain) |
| RA | 3,265,713 | G→A | P106S (CCA→TCA) | tdcB ← | catabolic threonine dehydratase |
| 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 | 3,481,880 | A→G | T198A (ACG→GCG) | yheS → | ABC transporter ATP‑binding protein YheS |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,639,916 | A→G | intergenic (‑196/‑195) | uspB ← / → uspA | putative universal stress (ethanol tolerance) protein B/universal stress global stress response regulator |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,840,018 | A→G | intergenic (‑25/‑197) | nlpA ← / → yicS | lipoprotein‑28/uncharacterized protein YicS |
| RA | 3,855,849 | T→C | H41R (CAC→CGC) | yidG ← | putative inner membrane protein |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 3,870,662 | T→C | T357A (ACC→GCC) | dgoT ← | putative D‑galactonate transporter |
| RA | 3,877,977 | G→A | P715S (CCG→TCG) | gyrB ← | DNA gyrase subunit B |
| RA | 3,931,183 | (G)7→6 | intergenic (‑90/‑133) | ravA ← / → kup | regulatory ATPase RavA/K(+):H(+) symporter Kup |
| RA | 3,970,032 | (G)6→7 | coding (1002/1047 nt) | wzzE → | enterobacterial common antigen polysaccharide co‑polymerase |
| RA | 3,982,103 | C→T | A406V (GCC→GTC) | yifK → | putative transporter YifK |
| RA | 4,026,879 | C→T | A118V (GCC→GTC) | fre → | flavin reductase |
| RA | 4,037,809 | (GT)5→4 | noncoding (291‑292/2905 nt) | rrlA → | 23S ribosomal RNA |
| RA | 4,122,367 | (G)7→8 | intergenic (‑80/+13) | hslV ← / ← ftsN | peptidase component of the HslVU protease/cell division protein FtsN |
| RA | 4,251,860 | (T)7→6 | pseudogene (1158/1581 nt) | yjbI → | pentapeptide repeats‑containing protein YjbI |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,372,012 | A→G | T330A (ACC→GCC) | groL → | chaperonin GroEL |
| RA | 4,385,046 | T→C | L403P (CTT→CCT) | yjeM → | putative transporter YjeM |
| RA | 4,410,177 | A→G | V15V (GTA→GTG) | yjfI → | conserved protein YjfI |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,464,564 | G→A | A49V (GCC→GTC) | treC ← | trehalose‑6‑phosphate hydrolase |
| RA | 4,475,152 | T→C | D97D (GAT→GAC) | tabA → | DUF386 domain‑containing toxin‑antitoxin biofilm protein TabA |
| RA | 4,535,811 | Δ1 bp | pseudogene (797/1017 nt) | yjhR → | KpLE2 phage‑like element; PLD‑like domain‑containing protein YjhR |
| RA | 4,556,769 | (T)9→8 | coding (116/144 nt) | ytiD → | protein YtiD |
| RA | 4,574,705 | A→G | pseudogene (571/2721 nt) | yjiV → | putative uncharacterized protein YjiV |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1465088 | 1465300 | 213 | 31 [28] | [29] 30 | ynbG | ynbG |
| * | * | ÷ | NC_000913 | 3423768–3424234 | 3424523–3424238 | 5–756 | 34 [29] | [19] 31 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3455386 | 3455625 | 240 | 34 [29] | [28] 30 | [gspA]–[gspC] | [gspA],[gspC] |
| * | * | ÷ | NC_000913 | 4304466 | 4304631 | 166 | 30 [28] | [29] 33 | [yjcS] | [yjcS] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 42 (0.450) | 79 (0.950) | 45/246 | 0.4 | 74.1% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 18 (0.220) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 42 (0.450) | 50 (0.600) | 35/246 | 1.0 | 64.5% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 18 (0.220) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 67 (0.730) | 49/270 | 0.5 | 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 = | 168 (1.790) | 135 (1.450) | 69/276 | 0.1 | 61.7% | 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) | 97 (1.030) | 56/278 | 0.3 | 92.4% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 8 (0.090) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||