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 | 400,937 | C→T | intergenic (‑14/‑449) | ddlA ← / → iraP | D‑alanine‑‑D‑alanine ligase A/anti‑adaptor protein IraP |
| 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 | 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 | 1,196,277 | C→T | N385N (AAC→AAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,280 | G→C | A386A (GCG→GCC) | icd → | isocitrate dehydrogenase |
| RA | 1,196,283 | A→G | K387K (AAA→AAG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,292 | C→T | T390T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,304 | G→A | E394E (GAG→GAA) | icd → | isocitrate dehydrogenase |
| RA | 1,196,316 | T→A | D398E (GAT→GAA) | icd → | isocitrate dehydrogenase |
| RA | 1,196,325 | A→G | K401K (AAA→AAG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,352 | C→A | D410E (GAC→GAA) | 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 | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| 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 | 1,352,193 | G→A | P148S (CCG→TCG) | sapF ← | putrescine ABC exporter ATP binding protein SapF |
| RA | 1,353,758 | T→A | D254V (GAT→GTT) | sapC ← | putrescine ABC exporter membrane protein SapC |
| RA | 1,355,904 | C→T | D403N (GAT→AAT) | sapA ← | putative periplasmic binding protein SapA |
| RA | 1,357,473 | C→T | V66I (GTA→ATA) | ymjA ← | DUF2543 domain‑containing protein YmjA |
| RA | 1,362,803 | C→T | R21C (CGC→TGC) | puuC → | gamma‑glutamyl‑gamma‑aminobutyraldehyde dehydrogenase |
| RA | 1,366,985 | C→T | G310R (GGG→AGG) | pspF ← | DNA‑binding transcriptional dual regulator PspF |
| RA | 1,382,845 | C→T | S300L (TCG→TTG) | ompG → | outer membrane porin G |
| RA | 1,440,381 | G→A | A135V (GCG→GTG) | ydbK ← | putative pyruvate‑flavodoxin oxidoreductase |
| 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 | 1,541,357 | C→T | E412K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,543,636 | C→T | G142D (GGT→GAT) | narU ← | nitrate/nitrite transporter NarU |
| RA | 1,547,154 | C→T | A6T (GCA→ACA) | yddG ← | amino acid exporter YddG |
| RA | 1,551,766 | C→T | F143F (TTC→TTT) | fdnI → | formate dehydrogenase N subunit gamma |
| RA | 1,552,228 | G→A | intergenic (+237/+170) | fdnI → / ← yddM | formate dehydrogenase N subunit gamma/DNA‑binding transcriptional regulator YddM |
| RA | 1,556,181 | C→T | D34N (GAT→AAT) | bdm ← | biofilm‑dependent modulation protein |
| RA | 1,565,918 | G→A | A408V (GCC→GTC) | dosC ← | diguanylate cyclase DosC |
| RA | 1,566,497 | G→A | A215V (GCT→GTT) | dosC ← | diguanylate cyclase DosC |
| RA | 1,567,076 | G→A | P22L (CCC→CTC) | dosC ← | diguanylate cyclase DosC |
| RA | 1,567,651 | G→A | N391N (AAC→AAT) | digH ← | divisome localized glycosyl hydrolase |
| RA | 1,568,442 | G→A | L128F (CTT→TTT) | digH ← | divisome localized glycosyl hydrolase |
| RA | 1,569,555 | G→A | P312L (CCT→CTT) | gadC ← | L‑glutamate:4‑aminobutyrate antiporter |
| RA | 1,579,410 | G→A | intergenic (‑68/‑135) | yddA ← / → yneP | ABC transporter family protein YddA/protein YneP |
| RA | 1,583,650 | G→A | A13V (GCC→GTC) | ydeO ← | DNA‑binding transcriptional dual regulator YdeO |
| RA | 1,585,196 | G→A | R431C (CGC→TGC) | ydeP ← | putative oxidoreductase YdeP |
| RA | 1,589,830 | T→C | N58D (AAC→GAC) | ydeT ← | fimbrial usher domain‑containing protein YdeT |
| 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 |
| 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 |
| JC JC | 1,907,615 | IS1 (+) +9 bp | intergenic (‑24/+638) | yobF ← / ← yebO | DUF2527 domain‑containing protein YobF/uncharacterized protein YebO |
| RA | 1,978,243 | G→T | intergenic (‑46/+275) | flhD ← / ← insB5 | DNA‑binding transcriptional dual regulator FlhD/IS1 family protein InsB |
| RA | 2,003,264 | C→T | E115K (GAA→AAA) | fliC ← | flagellar filament structural protein |
| RA | 2,032,423 | G→A | V219V (GTC→GTT) | yedJ ← | putative HD superfamily phosphohydrolase YedJ |
| RA | 2,095,057 | G→A | V175M (GTG→ATG) | hisH → | imidazole glycerol phosphate synthase subunit HisH |
| 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 | 2,342,582 | C→T | D530N (GAT→AAT) | yfaL ← | putative autotransporter adhesin YfaL |
| 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 | 3,102,348 | G→A | L169L (CTG→TTG) | trmB ← | tRNA m(7)G46 methyltransferase |
| RA | 3,199,005 | G→A | P213S (CCA→TCA) | glnE ← | fused glutamine synthetase deadenylase/glutamine synthetase adenylyltransferase |
| RA | 3,247,458 | C→T | intergenic (+30/‑210) | exuR → / → yqiM | DNA‑binding transcriptional repressor ExuR/protein YqiM |
| RA | 3,268,970 | A→G | T186A (ACA→GCA) | yhaC → | uncharacterized protein YhaC |
| RA | 3,308,736 | C→T | Q63Q (CAG→CAA) | nlpI ← | lipoprotein NlpI |
| RA | 3,324,164 | C→T | G250S (GGC→AGC) | folP ← | dihydropteroate synthase |
| RA | 3,355,173 | C→T | P150L (CCA→CTA) | gltB → | glutamate synthase subunit GltB |
| RA | 3,410,690 | C→T | T137T (ACC→ACT) | dusB → | tRNA‑dihydrouridine synthase B |
| RA | 3,450,107 | C→T | A43T (GCG→ACG) | rplV ← | 50S ribosomal subunit protein L22 |
| RA | 3,486,205 | C→A | T29K (ACG→AAG) | crp → | DNA‑binding transcriptional dual regulator CRP |
| RA | 3,491,417 | C→T | G16D (GGC→GAC) | fic ← | putative adenosine monophosphate‑‑protein transferase Fic |
| RA | 3,496,203 | A→G | K731K (AAA→AAG) | nirB → | nitrite reductase (NADH) large subunit |
| RA | 3,524,603 | C→T | A578V (GCG→GTG) | mrcA → | peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcA |
| RA | 3,528,272 | C→T | P602S (CCG→TCG) | igaA → | inner membrane protein IgaA |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| RA | 3,615,427 | C→T | P63S (CCG→TCG) | nikB → | Ni(2(+)) ABC transporter membrane subunit NikB |
| RA | 3,631,349 | C→T | K414K (AAG→AAA) | yhiJ ← | DUF4049 domain‑containing protein YhiJ |
| RA | 3,651,423 | C→T | pseudogene (133/746 nt) | yhiS → | putative uncharacterized protein YhiS |
| RA | 3,657,207 | C→T | N71N (AAC→AAT) | hdeD → | acid‑resistance membrane protein |
| RA | 3,673,046 | C→T | V211V (GTC→GTT) | rcdB → | putative DNA‑binding transcriptional regulator YhjC |
| MC JC | 3,682,261 | Δ34 bp | coding (1154‑1187/1287 nt) | dctA ← | C4 dicarboxylate/orotate:H(+) symporter |
| RA | 3,722,654 | C→T | A582T (GCG→ACG) | glyS ← | glycine‑‑tRNA ligase subunit beta |
| JC JC | 3,737,137 | IS2 (+) +5 bp | coding (37‑41/825 nt) | bax ← | putative glycoside hydrolase Bax |
| RA | 3,745,917 | C→T | P372S (CCG→TCG) | yiaN → | 2,3‑diketo‑L‑gulonate:Na(+) symporter ‑ membrane subunit |
| RA | 3,749,174 | C→T | P200S (CCG→TCG) | sgbH → | 3‑keto‑L‑gulonate‑6‑phosphate decarboxylase SgbH |
| RA | 3,758,605 | C→T | W419* (TGG→TGA) | selB ← | selenocysteyl‑tRNA‑specific translation elongation factor |
| RA | 3,771,296 | C→T | T28T (ACG→ACA) | yibH ← | inner membrane protein YibH |
| RA | 3,799,622 | C→T | G192D (GGT→GAT) | waaZ ← | lipopolysaccharide core biosynthesis protein WaaZ |
| RA | 3,805,424 | C→T | G176D (GGC→GAC) | waaP ← | lipopolysaccharide core heptose (I) kinase |
| RA | 3,828,128 | C→T | A180T (GCG→ACG) | gltS ← | glutamate:sodium symporter |
| RA | 3,832,051 | C→T | P532L (CCT→CTT) | yicH → | AsmA family protein YicH |
| RA | 3,838,773 | C→T | P176S (CCC→TCC) | yicL → | putative transporter YicL |
| RA | 3,844,413 | C→T | S150S (AGC→AGT) | adeD → | adenine deaminase |
| RA | 3,884,712 | C→T | R74C (CGT→TGT) | rnpA → | RNase P protein component |
| RA | 3,897,890 | C→T | L129L (CTG→TTG) | cbrB → | putative inner membrane protein |
| RA | 3,909,886 | G→A | L171L (CTC→CTT) | pstC ← | phosphate ABC transporter membrane subunit PstC |
| RA | 3,913,050 | G→A | L207F (CTT→TTT) | glmS ← | L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| RA | 3,996,126 | G→A | G182R (GGA→AGA) | yigA → | DUF484 domain‑containing protein YigA |
| RA | 3,997,278 | G→A | E32E (GAG→GAA) | yigB → | 5‑amino‑6‑(5‑phospho‑D‑ribitylamino)uracil phosphatase |
| RA | 4,012,789 | G→A | L10L (CTA→TTA) | metR ← | DNA‑binding transcriptional dual regulator MetR |
| RA | 4,016,990 | G→A | W187* (TGG→TAG) | udp → | uridine phosphorylase |
| RA | 4,032,219 | G→A | Q353Q (CAG→CAA) | pepQ → | Xaa‑Pro dipeptidase |
| RA | 4,034,217 | G→A | R358H (CGC→CAC) | trkH → | K(+) transporter TrkH |
| RA | 4,053,512 | G→A | intergenic (+94/+135) | hemN → / ← yshB | coproporphyrinogen III dehydrogenase/uncharacterized protein YshB |
| RA | 4,055,224 | G→A | L19F (CTT→TTT) | glnG ← | DNA‑binding transcriptional dual regulator NtrC |
| RA | 4,065,293 | G→A | R158R (CGC→CGT) | yihO ← | putative sulfoquinovose transporter |
| RA | 4,068,287 | G→A | F330F (TTC→TTT) | yihQ ← | sulfoquinovosidase |
| RA | 4,084,595 | G→A | L410F (CTC→TTC) | fdoG ← | formate dehydrogenase O subunit alpha |
| RA | 4,085,928 | G→A | intergenic (‑106/‑88) | fdoG ← / → fdhD | formate dehydrogenase O subunit alpha/sulfurtransferase for molybdenum cofactor sulfuration |
| RA | 4,091,821 | G→A | Y182Y (TAC→TAT) | frvB ← | putative PTS enzyme IIBC component FrvB |
| RA | 4,096,215 | G→A | L412L (CTA→TTA) | rhaB ← | rhamnulokinase |
| RA | 4,097,175 | G→A | Q92* (CAG→TAG) | rhaB ← | rhamnulokinase |
| RA | 4,099,805 | C→T | D241N (GAT→AAT) | rhaT ← | rhamnose/lyxose:H(+) symporter |
| RA | 4,115,968 | G→A | L419L (CTG→TTG) | glpK ← | glycerol kinase |
| JC JC | 4,123,923 | IS2 (–) +5 bp | coding (530‑534/1026 nt) | cytR ← | DNA‑binding transcriptional repressor CytR |
| RA | 4,132,970 | G→A | G119S (GGC→AGC) | metF → | 5,10‑methylenetetrahydrofolate reductase |
| 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 | 4,163,609 | G→A | intergenic (‑339/‑30) | trmA ← / → btuB | tRNA m(5)U54 methyltransferase/cobalamin outer membrane transporter |
| RA | 4,295,679 | G→A | G400D (GGT→GAT) | gltP → | glutamate/aspartate : H(+) symporter GltP |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| 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 | 4,542,683 | 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 | 1196365 | 1211435 | 15071 | 5 [3] | [4] 5 | [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 | 1978495 | 1979270 | 776 | 47 [0] | [0] 16 | insB5–insA5 | insB5,insA5 |
| * | * | ÷ | NC_000913 | 3423891–3424233 | 3424434–3424238 | 6–544 | 5 [4] | [3] 5 | rrlD | 23S ribosomal RNA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 381260 = | NA (NA) | 57 (1.470) | 56/490 | 0.0 | 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) | 25 (0.650) | 25/486 | 0.6 | NA | noncoding (920/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 382590 | NA (NA) | noncoding (1331/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 566774 | 36 (0.930) | 13 (0.340) | 7/486 | 2.5 | 28.1% | pseudogene (91/93 nt) | renD | protein RenD |
| ? | NC_000913 | 568036 = | 31 (0.810) | pseudogene (2/213 nt) | renD | protein RenD | |||||
| * | ? | NC_000913 | = 1397238 | NA (NA) | 47 (1.210) | 40/490 | 0.1 | 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 | 1979271 = | 0 (0.000) | 16 (0.410) | 15/490 | 1.3 | 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 | |||||
| * | ? | NC_000913 | = 3309172 | 14 (0.360) | 47 (1.210) | 44/490 | 0.1 | 77.7% | coding (1997/2136 nt) | pnp | polynucleotide phosphorylase |
| ? | NC_000913 | 3309188 = | 13 (0.340) | coding (1981/2136 nt) | pnp | polynucleotide phosphorylase | |||||