mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 99,678 | C→T | 5.2% | A12V (GCA→GTA) | murG → | N‑acetylglucosaminyl transferase |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 262,225 | G→T | 8.7% | V241V (GTG→GTT) | proA → | gamma‑glutamylphosphate reductase |
| RA | 349,717 | T→C | 6.2% | intergenic (+145/‑295) | prpB → / → prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
| RA | 606,958 | Δ1 bp | 5.1% | coding (426/1119 nt) | ybdK ← | weak gamma‑glutamyl:cysteine ligase |
| RA | 734,791 | A→G | 5.3% | pseudogene (659/1521 nt) | rhsO → | pseudogene, Rhs family |
| RA | 759,007 | T→G | 13.8% | F101C (TTC→TGC) | sucA → | 2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding |
| RA | 867,917 | T→C | 6.4% | L133P (CTG→CCG) | gsiA → | glutathione ABC transporter ATPase |
| RA | 1,039,722 | C→T | 6.1% | L143F (CTC→TTC) | cbdB → | cytochrome bd‑II oxidase, subunit II |
| RA | 1,054,863 | T→C | 5.1% | K439R (AAA→AGA) | torS ← | hybrid sensory histidine kinase in two‑component regulatory system with TorR |
| RA | 1,073,852 | G→A | 5.2% | Q54* (CAA→TAA) | rutA ← | pyrimidine oxygenase, FMN‑dependent |
| RA | 1,261,297 | G→T | 100% | D193E (GAC→GAA) | prs ← | phosphoribosylpyrophosphate synthase |
| RA | 1,261,471 | A→C | 8.8% | I135M (ATT→ATG) | prs ← | phosphoribosylpyrophosphate synthase |
| RA | 1,287,152 | T→C | 6.5% | noncoding (85/171 nt) T9A (ACT→GCT) |
rttR ← tpr ← |
rtT sRNA, processed from tyrT transcript protamine‑like protein |
| JC JC | 1,293,015 | IS1 (+) +8 bp | 5.1% | intergenic (‑93/‑505) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| JC JC | 1,293,091 | IS1 (+) +9 bp | 12.4% | intergenic (‑169/‑428) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| JC JC | 1,351,197 | IS186 (–) +6 bp :: Δ1 bp | 75.0% | intergenic (‑158/+205) | fabI ← / ← ycjD | enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent/DUF559 family endonuclease‑related protein |
| RA | 1,380,351 | G→A | 6.0% | S68S (TCG→TCA) | ycjU → | beta‑phosphoglucomutase |
| RA | 1,448,094 | Δ1 bp | 5.4% | coding (576/1500 nt) | feaB → | phenylacetaldehyde dehydrogenase |
| RA | 1,466,055 | G→T | 5.5% | pseudogene (664/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,508,007 | T→A | 5.2% | R409R (CGT→CGA) | ydcP → | putative peptidase |
| RA | 1,525,331 | T→C | 5.6% | H217R (CAC→CGC) | ansP ← | L‑asparagine transporter |
| RA | 1,557,347 | A→G | 5.9% | L231P (CTG→CCG) | ddpF ← | D,D‑dipeptide ABC transporter ATPase |
| RA | 1,708,930 | C→A | 24.1% | P671Q (CCG→CAG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| JC JC | 1,757,082 | IS5 (–) +4 bp | 26.2% | coding (1385‑1388/1413 nt) | pykF → | pyruvate kinase I |
| JC JC | 1,757,082 | IS5 (+) +4 bp | 64.7% | coding (1385‑1388/1413 nt) | pykF → | pyruvate kinase I |
| RA | 1,759,548 | A→G | 5.9% | Y326H (TAT→CAT) | sufS ← | cysteine desulfurase, stimulated by SufE; selenocysteine lyase, PLP‑dependent |
| RA | 1,797,774 | C→T | 6.8% | P57P (CCG→CCA) | pheT ← | phenylalanine tRNA synthetase, beta subunit |
| RA | 1,816,983 | A→G | 5.3% | R51R (CGT→CGC) | chbG ← | chito‑oligosaccharide deacetylase |
| RA | 1,974,817 | C→G | 5.1% | G170R (GGG→CGG) | cheA ← | fused chemotactic sensory histidine kinase in two‑component regulatory system with CheB and CheY: sensory histidine kinase/signal sensing protein |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,019,460 | G→A | 100% | V359I (GTC→ATC) | fliK → | flagellar hook‑length control protein |
| RA | 2,047,453 | C→T | 5.0% | T839I (ACT→ATT) | yeeJ → | putative adhesin |
| RA | 2,072,013 | C→T | 5.4% | H159Y (CAT→TAT) | flu → | CP4‑44 prophage; antigen 43 (Ag43) phase‑variable biofilm formation autotransporter |
| RA | 2,072,491 | C→T | 5.4% | T318M (ACG→ATG) | flu → | CP4‑44 prophage; antigen 43 (Ag43) phase‑variable biofilm formation autotransporter |
| RA | 2,076,294 | A→G | 5.2% | K506E (AAA→GAA) | yeeR → | CP4‑44 prophage; putative membrane protein |
| RA | 2,126,158 | A→T | 5.0% | F22Y (TTT→TAT) | wcaH ← | GDP‑mannose mannosyl hydrolase |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (1‑2/442 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,250,988 | A→T | 5.1% | D50V (GAT→GTT) | nfo → | endonuclease IV with intrinsic 3'‑5' exonuclease activity |
| RA | 2,263,235 | C→T | 6.9% | W87* (TGG→TGA) ‡ | fruB ← | fused fructose‑specific PTS enzymes: IIA component/HPr component |
| RA | 2,263,236 | C→G | 7.9% | W87S (TGG→TCG) ‡ | fruB ← | fused fructose‑specific PTS enzymes: IIA component/HPr component |
| RA | 2,263,237 | A→G | 5.8% | W87R (TGG→CGG) ‡ | fruB ← | fused fructose‑specific PTS enzymes: IIA component/HPr component |
| RA | 2,304,649 | C→T | 11.8% | intergenic (+256/+459) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,317,667 | T→G | 100% | E737A (GAA→GCA) | rcsC ← | hybrid sensory kinase in two‑component regulatory system with RcsB and YojN |
| RA | 2,367,945 | G→T | 16.1% | G292V (GGT→GTT) | arnC → | undecaprenyl phosphate‑L‑Ara4FN transferase |
| RA | 2,550,064 | T→C | 5.5% | K161R (AAA→AGA) | yfeX ← | porphyrinogen oxidase, cytoplasmic |
| RA | 2,560,985 | C→A | 17.4% | intergenic (+87/‑383) | yffL → / → yffM | CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein |
| RA | 2,569,416 | G→A | 5.2% | C32C (TGC→TGT) | eutG ← | ethanol dehydrogenase involved in ethanolamine utilization; aldehyde reductase |
| RA | 2,632,046 | G→T | 100% | P164T (CCG→ACG) | guaA ← | GMP synthetase (glutamine aminotransferase) |
| RA | 2,707,923 | G→A | 5.8% | R278C (CGC→TGC) | rseB ← | anti‑sigma E factor, binds RseA |
| JC JC | 2,867,796 | IS1 (+) +9 bp | 22.9% | coding (950‑958/1140 nt) | nlpD ← | activator of AmiC murein hydrolase activity, lipoprotein |
| RA | 2,969,920 | G→T | 5.4% | G87C (GGT→TGT) | mutH → | methyl‑directed mismatch repair protein |
| RA | 2,975,601 | T→G | 5.2% | E138D (GAA→GAC) | aas ← | fused 2‑acylglycerophospho‑ethanolamine acyl transferase/acyl‑acyl carrier protein synthetase |
| RA | 3,002,530 | G→A | 100% | G729D (GGT→GAT) | xdhA → | xanthine dehydrogenase, molybdenum binding subunit |
| RA | 3,056,551 | T→A | 6.4% | V104E (GTG→GAG) | fau → | 5‑formyltetrahydrofolate cyclo‑ligase family protein |
| RA | 3,231,792 | T→C | 6.4% | F43S (TTT→TCT) | fadH → | 2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked |
| RA | 3,269,917 | T→C | 7.0% | intergenic (+315/+299) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,270,194 | G→T | 6.8% | intergenic (+592/+22) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,270,195 | A→C | 10.1% | intergenic (+593/+21) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,270,196 | A→G | 7.1% | intergenic (+594/+20) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,391,321 | G→C | 6.4% | V236V (GTC→GTG) | tldD ← | putative peptidase |
| RA | 3,485,594 | G→A | 5.0% | R75R (CGC→CGT) | yhfA ← | OsmC family protein |
| RA | 3,560,455:1 | +G | 100% | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| RA | 3,608,695 | C→G | 6.6% | intergenic (+46/+56) | zntA → / ← tusA | zinc, cobalt and lead efflux system/mnm(5)‑s(2)U34‑tRNA 2‑thiolation sulfurtransferase |
| RA | 3,608,701 | A→C | 6.0% | intergenic (+52/+50) | zntA → / ← tusA | zinc, cobalt and lead efflux system/mnm(5)‑s(2)U34‑tRNA 2‑thiolation sulfurtransferase |
| JC JC | 3,890,075 | IS5 (–) +4 bp | 100% | coding (1346‑1349/1416 nt) | tnaA → | tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent |
| RA | 3,936,278 | A→G | 5.5% | M1M (ATG→GTG) † | rbsB → | D‑ribose ABC transporter periplasmic binding protein; ribose chemotaxis receptor |
| RA | 3,954,662 | C→T | 5.1% | C395C (TGC→TGT) | ilvD → | dihydroxyacid dehydratase |
| RA | 3,998,273 | G→A | 5.5% | L97L (TTG→TTA) | uvrD → | DNA‑dependent ATPase I and helicase II |
| RA | 4,296,060 | C→T | 37.9% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,305,438 | G→A | 5.3% | A387V (GCG→GTG) | yjcS ← | metallo‑beta‑lactamase superfamily protein |
| RA | 4,628,195 | A→G | 49.5% | Y294C (TAC→TGC) | nadR → | trifunctional protein: nicotinamide mononucleotide adenylyltransferase, ribosylnicotinamide kinase, transcriptional repressor |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423739–3424234 | 3424607–3424239 | 6–869 | 39 [35] | [37] 39 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3514373 | 3515114 | 742 | 38 [35] | [37] 39 | [gph]–[dam] | [gph],rpe,[dam] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 223995 | NA (NA) | 3 (0.030) | 3/256 | NT | NA | noncoding (225/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon |
| ? | NC_000913 | = 224006 | NA (NA) | noncoding (236/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | = 225530 | NA (NA) | 3 (0.030) | 3/256 | NT | NA | noncoding (31/76 nt) | alaV | tRNA‑Ala |
| ? | NC_000913 | = 225537 | NA (NA) | noncoding (38/76 nt) | alaV | tRNA‑Ala | |||||
| * | ? | NC_000913 | = 533547 | 86 (0.950) | 4 (0.050) | 3/230 | NT | 5.1% | coding (537/816 nt) | allR | glyoxylate‑inducible transcriptional repressor of all and gcl operons |
| ? | NC_000913 | = 533529 | 75 (0.960) | coding (519/816 nt) | allR | glyoxylate‑inducible transcriptional repressor of all and gcl operons | |||||
| * | ? | NC_000913 | = 1097463 | 14 (0.150) | 4 (0.050) | 5/250 | NT | 22.8% | intergenic (+634/+102) | ycdU/serX | putative inner membrane protein/tRNA‑Ser |
| ? | NC_000913 | = 1097467 | 14 (0.160) | intergenic (+638/+98) | ycdU/serX | putative inner membrane protein/tRNA‑Ser | |||||
| * | ? | NC_000913 | 1207790 = | 25 (0.280) | 35 (0.440) | 34/234 | NT | 57.4% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 30 (0.380) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 25 (0.280) | 39 (0.490) | 34/234 | NT | 60.0% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 30 (0.380) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 102 (1.160) | 77/258 | NT | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 1411899 = | 113 (1.250) | 6 (0.080) | 6/214 | NT | 7.1% | coding (50/936 nt) | ttcA | tRNA s(2)C32 thioltransferase, iron sulfur cluster protein |
| ? | NC_000913 | = 1434958 | 67 (0.920) | pseudogene (51/51 nt) | ttcC | pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1946997 | 57 (0.630) | 3 (0.030) | 3/254 | NT | 5.2% | coding (380/522 nt) | ruvC | component of RuvABC resolvasome, endonuclease |
| ? | NC_000913 | = 1947009 | 55 (0.640) | coding (368/522 nt) | ruvC | component of RuvABC resolvasome, endonuclease | |||||
| * | ? | NC_000913 | 4542682 = | 102 (1.120) | 11 (0.130) | 10/248 | NT | 8.9% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | 4542996 = | 129 (1.530) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | = 4542690 | 102 (1.120) | 12 (0.140) | 10/248 | NT | 9.7% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | = 4542986 | 129 (1.530) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||