mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| JC JC | 57,276 | IS2 (+) +5 bp | intergenic (‑167/‑84) | lptD ← / → djlA | lipopolysaccharide assembly protein LptD/co‑chaperone protein DjlA |
| RA | 71,134 | G→A | G250S (GGT→AGT) | araC → | DNA‑binding transcriptional dual regulator AraC |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 320,653 | G→A | A143T (GCA→ACA) | rclR → | DNA‑binding transcriptional activator RclR |
| RA | 323,514 | G→A | G393R (GGG→AGG) | ykgF → | putative amino acid dehydrogenase with NAD(P)‑binding domain and ferridoxin‑like domain |
| RA | 326,152 | G→A | P366S (CCA→TCA) | betA ← | choline dehydrogenase |
| RA | 360,774 | C→T | R261R (CGC→CGT) | cynX → | cyanate transporter |
| RA | 384,127 | C→T | V164I (GTT→ATT) | yaiS ← | putative deacetylase YaiS |
| RA | 466,049 | C→T | A422T (GCA→ACA) | ybaE ← | uncharacterized protein YbaE |
| RA | 475,410 | C→T | A11V (GCG→GTG) | ybaY → | PF09619 family lipoprotein YbaY |
| RA | 511,499 | C→T | intergenic (‑120/‑142) | copA ← / → glsA | Cu(+) exporting P‑type ATPase/glutaminase 1 |
| RA | 557,635 | A→T | L36Q (CTG→CAG) | folD ← | bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase |
| JC JC | 568,449 | IS2 (–) +5 bp | coding (135‑139/333 nt) | emrE → | multidrug/betaine/choline efflux transporter EmrE |
| RA | 631,633 | G→A | W580* (TGG→TGA) | cstA → | pyruvate transporter CstA |
| RA | 664,506 | G→A | P229S (CCG→TCG) | rlpA ← | rare lipoprotein RlpA |
| RA | 669,952 | G→A | N207N (AAC→AAT) | nadD ← | nicotinate‑nucleotide adenylyltransferase |
| RA | 674,367 | G→A | F139F (TTC→TTT) | leuS ← | leucine‑‑tRNA ligase |
| RA | 712,964 | C→T | intergenic (‑162/‑23) | ybfF ← / → seqA | esterase/negative modulator of initiation of replication |
| RA | 741,618 | G→A | F313F (TTC→TTT) | dtpD ← | dipeptide:H(+) symporter DtpD |
| RA | 910,820 | C→T | G77D (GGC→GAC) | poxB ← | pyruvate oxidase |
| RA | 987,152 | G→T | intergenic (‑170/+433) | ompF ← / ← asnS | outer membrane porin F/asparagine‑‑tRNA ligase |
| JC JC | 1,105,376 | IS2 (–) +5 bp | intergenic (+83/‑34) | csgC → / → ymdA | curlin chaperone/uncharacterized protein YmdA |
| 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 | 1,290,881 | C→T | L214F (CTT→TTT) | rssB → | regulator of RpoS |
| MC JC | 1,294,035 | Δ141 bp | [tdk] | [tdk] | |
| MC JC | 1,303,073 | Δ12 bp | coding (175‑186/921 nt) | oppB → | murein tripeptide ABC transporter/oligopeptide ABC transporter inner membrane subunit OppB |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| RA | 1,353,758 | T→A | D254V (GAT→GTT) | sapC ← | putrescine ABC exporter membrane protein SapC |
| RA | 1,354,849 | C→T | E208K (GAA→AAA) | sapB ← | putrescine ABC exporter membrane subunit SapB |
| RA | 1,440,873 | C→T | intergenic (‑89/‑185) | ydbK ← / → ydbJ | putative pyruvate‑flavodoxin oxidoreductase/DUF333 domain‑containing protein YdbJ |
| RA | 1,446,572 | C→T | G238S (GGT→AGT) | feaR ← | DNA‑binding transcriptional activator FeaR |
| RA | 1,466,824 | C→T | pseudogene (1433/2518 nt) | ydbA → | putative outer membrane protein, N‑terminal fragment |
| RA | 1,485,318 | C→T | A753V (GCG→GTG) | hrpA → | ATP‑dependent 3'‑>5' RNA helicase HrpA |
| RA | 1,494,388 | Δ1 bp | coding (684/924 nt) | ydcI ← | DNA‑binding transcriptional dual regulator YdcI |
| RA | 1,517,508 | G→T | V40V (GTG→GTT) | ortT → | orphan toxin OrtT |
| RA | 1,548,667 | C→T | R423C (CGT→TGT) | fdnG → | formate dehydrogenase N subunit alpha |
| RA | 1,617,534 | C→T | T169T (ACC→ACT) | ydeA → | L‑arabinose exporter |
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| RA | 1,667,887 | Δ1 bp | coding (678/1221 nt) | mlc ← | DNA‑binding transcriptional repressor Mlc |
| RA | 1,744,751 | Δ1 bp | coding (1295/1374 nt) | mdtK → | multidrug efflux pump MdtK |
| RA | 1,762,757 | G→A | T418I (ACC→ATC) | sufB ← | Fe‑S cluster scaffold complex subunit SufB |
| RA | 1,764,707 | G→A | intergenic (‑321/+6) | sufA ← / ← rydB | iron‑sulfur cluster insertion protein SufA/small regulatory RNA RydB |
| JC JC | 1,792,772 | IS2 (–) +5 bp | intergenic (‑41/+33) | nlpC ← / ← btuD | NlpC/P60 family lipoprotein NlpC/vitamin B12 ABC transporter ATP binding subunit |
| RA | 1,809,137 | G→A | L33L (CTG→TTG) | yniB ← | uncharacterized protein YniB |
| RA | 1,822,846 | G→A | S130N (AGC→AAC) | nadE → | NH3‑dependent NAD(+) synthetase |
| RA | 1,824,672 | G→A | A89V (GCG→GTG) | ves ← | HutD family protein Ves |
| RA | 1,827,165 | G→A | C365C (TGC→TGT) | astB ← | N‑succinylarginine dihydrolase |
| RA | 1,844,291 | G→A | A194V (GCC→GTC) | ynjI ← | DUF1266 domain‑containing protein YnjI |
| RA | 1,894,331 | G→A | V67I (GTT→ATT) | yoaC → | DUF1889 domain‑containing protein YoaC |
| RA | 1,906,163 | G→A | G159D (GGC→GAC) | mntP → | Mn(2(+)) exporter |
| RA | 1,925,529 | G→A | R30R (AGG→AGA) | yobB → | putative carbon‑nitrogen hydrolase family protein YobB |
| RA | 1,929,785 | G→A | intergenic (‑78/+249) | yebE ← / ← yebF | DUF533 domain‑containing inner membrane protein YebE/secreted protein YebF |
| RA | 1,978,243 | G→T | intergenic (‑46/+275) | flhD ← / ← insB5 | DNA‑binding transcriptional dual regulator FlhD/IS1 family protein InsB |
| RA | 1,987,300 | G→A | E126K (GAA→AAA) | ftnB → | putative ferritin‑like protein |
| RA | 1,995,073 | G→A | A96V (GCC→GTC) | uvrY ← | DNA‑binding transcriptional activator UvrY |
| RA | 2,003,264 | C→T | E115K (GAA→AAA) | fliC ← | flagellar filament structural protein |
| RA | 2,014,421 | A→G | N398S (AAC→AGC) | fliF → | flagellar basal‑body MS‑ring and collar protein |
| RA | 2,016,917 | G→A | D122N (GAC→AAC) | fliI → | flagellar export ATPase FliI |
| RA | 2,020,842 | C→T | R252R (CGC→CGT) | fliM → | flagellar motor switch protein FliM |
| RA | 2,026,128 | C→T | R206R (CGC→CGT) | yedP → | putative mannosyl‑3‑phosphoglycerate phosphatase |
| RA | 2,061,614 | G→A | T107I (ACC→ATC) | nac ← | DNA‑binding transcriptional dual regulator Nac |
| RA | 2,173,363 | Δ2 bp | intergenic (‑490/+918) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| RA | 2,242,121 | A→G | S283P (TCG→CCG) | yeiB ← | DUF418 domain‑containing protein YeiB |
| JC JC | 2,269,876 | IS5 (+) +4 bp | intergenic (+309/‑100) | lpxT → / → mepS | lipid A‑core phosphotransferase/peptidoglycan endopeptidase/peptidoglycan L,D‑carboxypeptidase |
| JC JC | 2,319,850 | IS2 (+) +5 bp | coding (23‑27/2850 nt) | rcsC ← | histidine kinase RcsC |
| RA | 2,397,444 | G→A | Q908* (CAA→TAA) | nuoG ← | NADH:quinone oxidoreductase subunit G |
| JC JC | 2,406,780 | IS1 (–) +8 bp | intergenic (‑139/‑774) | lrhA ← / → alaA | DNA‑binding transcriptional dual regulator LrhA/glutamate‑‑pyruvate aminotransferase AlaA |
| MC JC | 2,558,699 | Δ6,790 bp | intZ–[eutA] | intZ, yffL, yffM, yffN, yffO, yffP, yffQ, yffR, yffS, [eutA] | |
| JC JC | 2,666,074 | IS1 (+) +9 bp | coding (640‑648/1281 nt) | csiE → | stationary phase‑inducible protein CsiE |
| RA | 3,133,781 | C→T | W59* (TGG→TGA) | yghS ← | putative ATP‑binding protein YghS |
| RA | 3,196,387 | C→T | E123K (GAA→AAA) | hldE ← | fused heptose 7‑phosphate kinase/heptose 1‑phosphate adenyltransferase |
| RA | 3,259,361 | G→A | P97S (CCA→TCA) | tdcG ← | L‑serine deaminase III |
| RA | 3,260,993 | C→T | D476N (GAT→AAT) | tdcE ← | 2‑ketobutyrate formate‑lyase/pyruvate formate‑lyase 4 |
| RA | 3,262,684 | C→T | G326E (GGA→GAA) | tdcD ← | propionate kinase |
| RA | 3,268,970 | A→G | T186A (ACA→GCA) | yhaC → | uncharacterized protein YhaC |
| RA | 3,279,871 | C→T | L320L (CTG→TTG) | kbaZ → | putative tagatose‑1,6‑bisphosphate aldolase 1 chaperone |
| RA | 3,287,098 | G→A | intergenic (+73/‑328) | agaI → / → yraH | putative deaminase AgaI/putative fimbrial protein YraH |
| RA | 3,351,225 | G→A | P601S (CCG→TCG) | arcB ← | sensor histidine kinase ArcB |
| RA | 3,443,461 | C→T | G213S (GGC→AGC) | secY ← | Sec translocon subunit SecY |
| RA | 3,486,205 | C→A | T29K (ACG→AAG) | crp → | DNA‑binding transcriptional dual regulator CRP |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| RA | 3,568,113 | G→A | R406C (CGT→TGT) | glgC ← | glucose‑1‑phosphate adenylyltransferase |
| RA | 3,572,984 | G→A | G173G (GGC→GGT) | glgB ← | 1,4‑alpha‑glucan branching enzyme |
| RA | 3,575,673 | G→A | intergenic (+9/+48) | yhgN → / ← gntU | MarC family putative inner membrane protein YhgN/low‑affinity gluconate transporter |
| RA | 3,583,267 | G→A | pseudogene (230/390 nt) | yrhA → | putative uncharacterized protein YrhA |
| RA | 3,614,434 | G→A | Q256Q (CAG→CAA) | nikA → | Ni(2(+)) ABC transporter periplasmic binding protein |
| RA | 3,632,188 | G→A | L135F (CTT→TTT) | yhiJ ← | DUF4049 domain‑containing protein YhiJ |
| RA | 3,656,351 | G→A | intergenic (‑59/+57) | hdeB ← / ← hdeA | periplasmic acid stress chaperone HdeB/periplasmic acid stress chaperone HdeA |
| RA | 3,702,802 | G→A | P23S (CCG→TCG) | dppF ← | dipeptide ABC transporter ATP binding subunit DppF |
| RA | 3,711,620 | G→A | P130S (CCG→TCG) | yhjX ← | putative transporter YhjX |
| RA | 3,733,008 | G→A | V270I (GTT→ATT) | xylG → | xylose ABC transporter ATP binding subunit |
| RA | 3,733,520 | G→A | A440A (GCG→GCA) | xylG → | xylose ABC transporter ATP binding subunit |
| RA | 3,735,324 | G→A | E116K (GAG→AAG) | xylR → | DNA‑binding transcriptional dual regulator XylR |
| JC JC | 3,737,137 | IS2 (+) +5 bp | coding (37‑41/825 nt) | bax ← | putative glycoside hydrolase Bax |
| RA | 3,740,265 | G→A | R187R (CGG→CGA) | avtA → | valine‑‑pyruvate aminotransferase |
| RA | 3,758,146 | G→A | F572F (TTC→TTT) | selB ← | selenocysteyl‑tRNA‑specific translation elongation factor |
| RA | 3,758,201 | G→A | A554V (GCC→GTC) | selB ← | selenocysteyl‑tRNA‑specific translation elongation factor |
| RA | 3,783,813 | G→A | L106L (CTG→TTG) | secB ← | protein export chaperone SecB |
| RA | 3,791,877 | G→A | S225S (TCC→TCT) | kbl ← | 2‑amino‑3‑ketobutyrate CoA ligase |
| RA | 3,794,662 | G→A | E226K (GAA→AAA) | rfaD → | ADP‑L‑glycero‑D‑mannoheptose 6‑epimerase |
| RA | 3,800,088 | G→A | P37S (CCT→TCT) | waaZ ← | lipopolysaccharide core biosynthesis protein WaaZ |
| RA | 3,800,629 | G→A | R113C (CGT→TGT) | waaY ← | lipopolysaccharide core heptose (II) kinase |
| RA | 3,810,916 | G→A | R79R (CGC→CGT) | mutM ← | DNA‑formamidopyrimidine glycosylase |
| RA | 3,817,246 | G→A | D191N (GAT→AAT) | yicC → | putative RNase adaptor protein YicC |
| RA | 3,857,408 | G→A | P333S (CCG→TCG) | yidJ ← | putative sulfatase/phosphatase YidJ |
| RA | 3,862,357 | G→A | P39L (CCG→CTG) | glvB ← | putative PTS enzyme II component GlvB |
| RA | 3,871,025 | G→A | L236L (CTG→TTG) | dgoT ← | D‑galactonate:H(+) symporter |
| RA | 3,886,834 | G→A | D3N (GAT→AAT) | mnmE → | 5‑carboxymethylaminomethyluridine‑tRNA synthase GTPase subunit |
| RA | 3,893,219 | G→A | G152D (GGT→GAT) | yidZ → | DNA‑binding transcriptional dual regulator YidZ |
| RA | 3,895,120 | G→A | D157N (GAT→AAT) | yieF → | quinone reductase |
| RA | 3,933,540 | G→A | V64I (GTC→ATC) | rbsD → | D‑ribose pyranase |
| RA | 3,947,803 | G→A | I55I (ATC→ATT) | hdfR ← | DNA‑binding transcriptional dual regulator HdfR |
| RA | 4,014,729 | C→T | L559L (CTC→CTT) | metE → | cobalamin‑independent homocysteine transmethylase |
| JC JC | 4,123,923 | IS2 (–) +5 bp | coding (530‑534/1026 nt) | cytR ← | DNA‑binding transcriptional repressor CytR |
| JC JC | 4,135,180 | IS2 (–) +5 bp | coding (1346‑1350/2181 nt) | katG → | catalase/hydroperoxidase HPI |
| RA | 4,146,389 | (T)6→7 | coding (132/879 nt) | pflC → | putative pyruvate formate‑lyase 2 activating enzyme PflC |
| RA | 4,215,045 | G→A | D256N (GAC→AAC) | metA → | homoserine O‑succinyltransferase |
| RA | 4,223,217 | C→T | V138I (GTA→ATA) | iclR ← | DNA‑binding transcriptional repressor IclR |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,296,591 | C→T | G179S (GGT→AGT) | yjcO ← | Sel1 repeat‑containing protein YjcO |
| RA | 4,406,491 | C→T | A101V (GCC→GTC) | nsrR → | DNA‑binding transcriptional regulator NsrR |
| RA | 4,410,466 | C→T | L112F (CTT→TTT) | yjfI → | DUF2170 domain‑containing protein YjfI |
| RA | 4,415,263 | C→T | P330L (CCA→CTA) | aidB → | putative acyl‑CoA dehydrogenase AidB |
| RA | 4,415,277 | C→T | P335S (CCC→TCC) | aidB → | putative acyl‑CoA dehydrogenase AidB |
| RA | 4,460,386 | C→T | intergenic (‑22/+136) | nrdG ← / ← nrdD | anaerobic ribonucleoside‑triphosphate reductase activating protein/anaerobic ribonucleoside‑triphosphate reductase |
| RA | 4,478,709 | C→T | I79I (ATC→ATT) | rraB → | ribonuclease E inhibitor protein B |
| RA | 4,512,213 | C→T | A68T (GCG→ACG) | fecD ← | ferric citrate ABC transporter membrane subunit FecD |
| RA | 4,519,679 | C→T | A216T (GCC→ACC) | yjhU ← | putative DNA‑binding transcriptional regulator YjhU |
| JC JC | 4,536,236 | IS5 (+) +4 bp | intergenic (‑2183/‑358) | topAI ← / → ythB | toxin of the TopAI‑YjhQ toxin‑antitoxin system, TopA inhibitor/protein YthB |
| RA | 4,537,230 | C→T | G122E (GGA→GAA) | nanS ← | N‑acetyl‑9‑O‑acetylneuraminate esterase |
| RA | 4,542,683 | Δ1 bp | intergenic (+50/‑432) | fimE → / → fimA | regulator for fimA/type 1 fimbriae major subunit |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 289229 | 289275 | 47 | 2 [1] | [0] 2 | xynR/argF | DNA‑binding transcriptional repressor XynR/ornithine carbamoyltransferase ArgF |
| * | * | ÷ | NC_000913 | 872072 | 872129 | 58 | 2 [0] | [1] 2 | gsiD | glutathione ABC transporter membrane subunit GsiD |
| * | * | ÷ | NC_000913 | 975832 | 975866 | 35 | 3 [1] | [1] 2 | mukE | chromosome partitioning protein MukE |
| * | * | ÷ | NC_000913 | 1194473 | 1194530 | 58 | 2 [1] | [1] 2 | rluE | 23S rRNA pseudouridine(2457) synthase |
| * | * | ÷ | NC_000913 | 1196363 | 1211421 | 15059 | 2 [1] | [1] 2 | [icd]–mcrA | [icd],C0293,ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,ymfN,ymfR,beeE,ymfQ,ycfK,tfaP,tfaE,pinE,mcrA |
| * | * | ÷ | NC_000913 | 1299494 | 1300695 | 1202 | 2 [1] | [1] 2 | insH21 | insH21 |
| * | * | ÷ | NC_000913 | 1386764 | 1386819 | 56 | 2 [1] | [1] 2 | tyrR | DNA‑binding transcriptional dual regulator TyrR |
| * | * | ÷ | NC_000913 | 1968195 | 1968213 | 19 | 2 [1] | [1] 2 | cheB | protein‑glutamate methylesterase/protein glutamine deamidase |
| * | * | ÷ | NC_000913 | 1978495 | 1979270–1978503 | 9–776 | 17 [0] | [0] 11 | insB5–insA5 | insB5,insA5 |
| * | * | ÷ | NC_000913 | 2673608 | 2673624 | 17 | 2 [1] | [1] 3 | yphA | putative inner membrane protein |
| * | * | ÷ | NC_000913 | 2799868 | 2799910 | 43 | 3 [1] | [1] 2 | ygaC | DUF2002 domain‑containing protein YgaC |
| * | * | ÷ | NC_000913 | 3045995 | 3046139 | 145 | 2 [1] | [1] 2 | ygfF/gcvP | putative oxidoreductase YgfF/glycine decarboxylase |
| * | * | ÷ | NC_000913 | 3423879–3424228 | 3424442–3424240 | 13–564 | 2 [1] | [1] 2 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 3682261 | 3682303 | 43 | 2 [0] | [1] 2 | dctA | C4 dicarboxylate/orotate:H(+) symporter |
| * | * | ÷ | NC_000913 | 3908498 | 3908539 | 42 | 2 [1] | [1] 3 | pstB/pstA | phosphate ABC transporter ATP binding subunit/phosphate ABC transporter membrane subunit PstA |
| * | * | ÷ | NC_000913 | 4294620 | 4294650 | 31 | 2 [0] | [1] 2 | gltP | glutamate/aspartate : H(+) symporter GltP |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 381260 = | NA (NA) | 13 (1.000) | 12/290 | 0.1 | NA | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 382183 | NA (NA) | noncoding (924/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 382179 = | NA (NA) | 15 (1.170) | 11/286 | 0.1 | NA | noncoding (920/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 382590 | NA (NA) | noncoding (1331/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 1397238 | NA (NA) | 17 (1.310) | 14/290 | 0.0 | 100% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 1978494 | 0 (0.000) | intergenic (‑297/+24) | flhD/insB5 | DNA‑binding transcriptional dual regulator FlhD/IS1 family protein InsB | |||||
| * | ? | NC_000913 | 1907618 = | 4 (0.310) | 13 (1.010) | 8/286 | 0.3 | 76.5% | intergenic (‑27/+643) | yobF/yebO | DUF2527 domain‑containing protein YobF/uncharacterized protein YebO |
| ? | NC_000913 | = 1979270 | NA (NA) | noncoding (1/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | 1979271 = | 0 (0.000) | 11 (0.840) | 10/290 | 0.2 | 100% | intergenic (‑56/‑482) | insA5/uspC | IS1 family protein InsA/universal stress protein C |
| ? | NC_000913 | = 2102947 | NA (NA) | pseudogene (443/446 nt) | wbbL | interrupted rhamnosyltransferase WbbL | |||||