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 | 71,033 | G→A | 5.5% | R216H (CGC→CAC) | araC → | ara regulon transcriptional activator; autorepressor |
| RA | 77,914 | A→G | 5.3% | A98A (GCA→GCG) | setA → | broad specificity sugar efflux system |
| RA | 92,684 | A→T | 5.1% | T424T (ACA→ACT) | ftsI → | transpeptidase involved in septal peptidoglycan synthesis; penicillin‑binding protein 3 |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 262,059 | A→G | 5.1% | E186G (GAA→GGA) | proA → | gamma‑glutamylphosphate reductase |
| RA | 298,093 | A→G | 5.5% | S212P (TCA→CCA) | paoD ← | moco insertion factor for PaoABC aldehyde oxidoreductase |
| RA | 450,001 | T→C | 6.3% | K214R (AAG→AGG) | cyoB ← | cytochrome o ubiquinol oxidase subunit I |
| RA | 465,367 | G→A | 5.9% | L61L (CTG→TTG) | queC ← | 7‑cyano‑7‑deazaguanine (preQ0) synthase; queuosine biosynthesis |
| RA | 548,669 | A→T | 5.7% | T105S (ACT→TCT) | ylbE → | NO‑induced DUF1116 protein |
| RA | 550,098 | T→C | 6.1% | W158R (TGG→CGG) | ylbF → | putative anaerobic allantoin catabolic oxamate carbamoyltransferase; DUF2877 family protein |
| RA | 797,175 | A→G | 5.5% | K208E (AAA→GAA) | modC → | molybdate ABC transporter ATPase; chlorate resistance protein |
| RA | 880,369 | T→C | 6.6% | I38V (ATA→GTA) | gstB ← | glutathione S‑transferase |
| RA | 909,753 | Δ1 bp | 7.3% | coding (1297/1719 nt) | poxB ← | pyruvate dehydrogenase, thiamine triphosphate‑binding, FAD‑binding |
| RA | 984,677 | T→A | 6.3% | N345Y (AAC→TAC) | aspC ← | aspartate aminotransferase, PLP‑dependent |
| RA | 1,024,226 | G→A | 5.2% | C41C (TGC→TGT) | yccF ← | DUF307 family inner membrane protein |
| RA | 1,024,286 | C→T | 9.1% | W21* (TGG→TGA) | yccF ← | DUF307 family inner membrane protein |
| RA | 1,052,257 | C→T | 5.7% | intergenic (+17/+32) | gnsA → / ← yccM | putative phosphatidylethanolamine synthesis regulator/putative 4Fe‑4S membrane protein |
| RA | 1,052,260 | T→C | 6.0% | intergenic (+20/+29) | gnsA → / ← yccM | putative phosphatidylethanolamine synthesis regulator/putative 4Fe‑4S membrane protein |
| RA | 1,052,261 | G→A | 5.9% | intergenic (+21/+28) | gnsA → / ← yccM | putative phosphatidylethanolamine synthesis regulator/putative 4Fe‑4S membrane protein |
| RA | 1,052,264 | A→G | 5.8% | intergenic (+24/+25) | gnsA → / ← yccM | putative phosphatidylethanolamine synthesis regulator/putative 4Fe‑4S membrane protein |
| RA | 1,077,912 | G→A | 6.6% | P324L (CCG→CTG) | putA ← | fused DNA‑binding transcriptional regulator/proline dehydrogenase/pyrroline‑5‑carboxylate dehydrogenase |
| RA | 1,115,605 | A→C | 6.2% | intergenic (‑115/+57) | mdtG ← / ← lpxL | putative drug efflux system protein/lauryl‑acyl carrier protein (ACP)‑dependent acyltransferase |
| RA | 1,132,502 | G→A | 7.1% | G217S (GGC→AGC) | flgD → | flagellar hook assembly protein |
| RA | 1,135,548 | T→C | 5.3% | intergenic (+37/‑16) | flgG → / → flgH | flagellar component of cell‑distal portion of basal‑body rod/flagellar protein of basal‑body outer‑membrane L ring |
| RA | 1,162,698:1 | +T | 6.6% | coding (61/642 nt) | lpoB → | OM lipoprotein stimulator of MrcB transpeptidase |
| RA | 1,281,264 | C→T | 7.5% | S467S (AGC→AGT) | narG → | nitrate reductase 1, alpha subunit |
| RA | 1,466,138 | G→A | 6.6% | pseudogene (747/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,144 | G→T | 6.3% | pseudogene (753/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,539,455 | G→A | 5.8% | Q1046* (CAG→TAG) | narZ ← | nitrate reductase 2 (NRZ), alpha subunit |
| RA | 1,595,045 | C→A | 6.5% | pseudogene (2943/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,614,751 | T→C | 5.0% | intergenic (‑48/‑53) | sad ← / → yneJ | succinate semialdehyde dehydrogenase, NAD(P)+‑dependent/putative DNA‑binding transcriptional regulator |
| RA | 1,708,662 | C→G | 14.3% | Q582E (CAA→GAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,751 | A→G | 24.2% | E611E (GAA→GAG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,994 | A→C | 19.3% | A692A (GCA→GCC) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,709,038 | T→A | 8.9% | V707E (GTA→GAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,797,390 | C→G | 6.2% | L185L (CTG→CTC) | pheT ← | phenylalanine tRNA synthetase, beta subunit |
| RA | 1,830,112 | G→C | 7.4% | S218S (TCC→TCG) | astA ← | arginine succinyltransferase |
| RA | 1,912,153 | T→C | 5.3% | S142G (AGC→GGC) | htpX ← | putative endopeptidase |
| RA | 1,934,584 | G→A | 6.2% | R7R (CGC→CGT) | edd ← | 6‑phosphogluconate dehydratase |
| RA | 1,964,653 | A→T | 5.6% | L133H (CTC→CAC) | flhA ← | putative flagellar export pore protein |
| RA | 1,968,056 | G→A | 6.6% | A149V (GCG→GTG) | cheB ← | fused chemotaxis regulator: protein‑glutamate methylesterase in two‑component regulatory system with CheA |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 1,982,787 | T→C | 6.2% | I252V (ATT→GTT) | araH ← | L‑arabinose ABC transporter permease |
| RA | 1,993,134 | G→C | 5.6% | P525A (CCC→GCC) | uvrC ← | excinuclease UvrABC, endonuclease subunit |
| RA | 2,009,731 | A→G | 5.3% | intergenic (+19/‑90) | yedF → / → yedK | putative TusA family sulfurtransferase/DUF159 family protein |
| RA | 2,009,732 | C→G | 5.3% | intergenic (+20/‑89) | yedF → / → yedK | putative TusA family sulfurtransferase/DUF159 family protein |
| RA | 2,019,460 | G→A | 100% | V359I (GTC→ATC) | fliK → | flagellar hook‑length control protein |
| RA | 2,029,851 | A→G | 8.7% | T105A (ACC→GCC) | yedA → | amino acid exporter for phenylalanine, threonine |
| RA | 2,060,804 | A→G | 5.3% | I37I (ATT→ATC) | cbl ← | ssuEADCB/tauABCD operon transcriptional activator |
| RA | 2,084,930 | T→A | 5.9% | H199L (CAT→CTT) | yeeE ← | UPF0394 family inner membrane protein |
| JC JC | 2,099,835 | IS1 (+) +8 bp | 66.3% | intergenic (‑222/+20) | ugd ← / ← gnd | UDP‑glucose 6‑dehydrogenase/6‑phosphogluconate dehydrogenase, decarboxylating |
| 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 | 2,263,951 | C→T | 6.5% | A30V (GCG→GTG) | setB → | lactose/glucose efflux system |
| RA | 2,317,667 | T→G | 100% | E737A (GAA→GCA) | rcsC ← | hybrid sensory kinase in two‑component regulatory system with RcsB and YojN |
| RA | 2,400,119 | G→A | 5.0% | A16V (GCG→GTG) | nuoG ← | NADH:ubiquinone oxidoreductase, chain G |
| RA | 2,428,707 | C→T | 7.1% | intergenic (‑81/+14) | ubiX ← / ← purF | 3‑octaprenyl‑4‑hydroxybenzoate carboxy‑lyase/amidophosphoribosyltransferase |
| RA | 2,510,349 | C→T | 5.4% | A240A (GCC→GCT) | yfeO → | putative ion channel protein |
| RA | 2,512,378 | A→G | 5.3% | L110P (CTG→CCG) | mntH ← | manganese/divalent cation transporter |
| RA | 2,560,996 | G→T | 23.2% | intergenic (+98/‑372) | yffL → / → yffM | CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein |
| RA | 2,569,859 | G→A | 6.0% | T160M (ACG→ATG) | eutJ ← | ethanolamine utilization protein, HSP70/actin superfamily protein |
| RA | 2,570,524 | C→T | 6.4% | A410T (GCT→ACT) | eutE ← | aldehyde oxidoreductase, ethanolamine utilization protein |
| RA | 2,612,520 | C→A | 5.6% | C207* (TGC→TGA) | hyfR → | hydrogenase‑4 transcriptional activator |
| RA | 2,632,046 | G→T | 100% | P164T (CCG→ACG) | guaA ← | GMP synthetase (glutamine aminotransferase) |
| RA | 2,641,450 | G→T | 9.6% | R119S (CGC→AGC) | ispG ← | 1‑hydroxy‑2‑methyl‑2‑(E)‑butenyl 4‑diphosphate synthase |
| RA | 2,649,813 | T→A | 5.5% | L825F (TTA→TTT) | yfhM ← | bacterial alpha2‑macroglobulin colonization factor ECAM; anti‑host protease defense factor; periplasmic inner membrane‑anchored lipoprotein |
| RA | 2,690,411 | G→A | 6.7% | R230C (CGC→TGC) | glrK ← | sensor protein kinase regulating glmY sRNA in two‑component system with response regulator GlrR |
| JC JC | 2,868,098 | IS5 (+) +4 bp | 94.4% | coding (653‑656/1140 nt) | nlpD ← | activator of AmiC murein hydrolase activity, lipoprotein |
| RA | 2,896,884 | A→T | 6.4% | C329* (TGT→TGA) | ygcS ← | putative MFS sugar transporter; membrane protein |
| RA | 3,002,530 | G→A | 100% | G729D (GGT→GAT) | xdhA → | xanthine dehydrogenase, molybdenum binding subunit |
| RA | 3,075,097 | C→T | 5.4% | G33G (GGG→GGA) | yggD ← | MtlR family putative transcriptional repressor |
| RA | 3,085,902 | C→T | 5.3% | D4N (GAC→AAC) | speA ← | biosynthetic arginine decarboxylase, PLP‑binding |
| RA | 3,223,594 | A→T | 5.1% | K321I (AAA→ATA) | ebgA → | evolved beta‑D‑galactosidase, alpha subunit |
| RA | 3,270,030 | T→C | 13.3% | intergenic (+428/+186) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,339,930 | C→T | 5.1% | G46S (GGT→AGT) | mlaF ← | ABC transporter maintaining OM lipid asymmetry, ATP‑binding protein |
| RA | 3,358,010 | C→T | 17.2% | P1096S (CCG→TCG) | gltB → | glutamate synthase, large subunit |
| RA | 3,372,270 | C→G | 5.1% | C102S (TGC→TCC) | nanT ← | sialic acid transporter |
| RA | 3,439,728 | G→T | 5.0% | A91D (GCC→GAC) | rplQ ← | 50S ribosomal subunit protein L17 |
| RA | 3,547,815 | G→A | 6.1% | L419L (CTG→CTA) | gntT → | gluconate transporter, high‑affinity GNT I system |
| 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 | 3,566,711 | C→T | 5.7% | L441L (CTG→CTA) | glgA ← | glycogen synthase |
| RA | 3,781,103 | A→C | 12.5% | intergenic (+86/‑112) | lldD → / → trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| RA | 3,806,430 | C→A | 5.6% | R213L (CGC→CTC) | waaG ← | UDP‑glucose:(heptosyl)lipopolysaccharide alpha‑1,3‑glucosyltransferase; lipopolysaccharide core biosynthesis protein; lipopolysaccharide glucosyltransferase I |
| JC JC | 3,890,075 | IS5 (–) +4 bp | 100% | coding (1346‑1349/1416 nt) | tnaA → | tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent |
| RA | 3,926,339 | C→T | 5.4% | P39P (CCG→CCA) | mioC ← | FMN‑binding protein MioC |
| RA | 4,054,925 | A→G | 6.7% | A118A (GCT→GCC) | glnG ← | fused DNA‑binding response regulator in two‑component regulatory system with GlnL: response regulator/sigma54 interaction protein |
| RA | 4,083,441 | C→T | 5.8% | P794P (CCG→CCA) | fdoG ← | formate dehydrogenase‑O, large subunit |
| RA | 4,095,330 | G→A | 6.5% | P218L (CCT→CTT) | rhaA ← | L‑rhamnose isomerase |
| RA | 4,184,578 | A→C | 18.2% | I1112L (ATC→CTC) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,186,607 | C→T | 67.5% | P420S (CCG→TCG) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,236,541 | A→T | 5.6% | T94S (ACT→TCT) | yjbF → | extracellular polysaccharide production lipoprotein |
| RA | 4,296,060 | C→T | 29.1% | 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 |
| MC JC | 4,309,624 | Δ3,364 bp | 100% | [alsA]–[alsR] | [alsA], alsB, [alsR] | |
| RA | 4,409,836 | A→G | 5.2% | T188A (ACC→GCC) | rlmB → | 23S rRNA mG2251 2'‑O‑ribose methyltransferase, SAM‑dependent |
| RA | 4,463,293 | T→A | 6.0% | T473S (ACA→TCA) | treC ← | trehalose‑6‑P hydrolase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423745–3424547 | 3424547 | 1–803 | 27 [26] | [26] 28 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3514388 | 3515102 | 715 | 27 [24] | [26] 27 | [gph]–[dam] | [gph],[rpe],[dam] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 22 (0.260) | 42 (0.580) | 36/228 | NT | 62.1% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 32 (0.440) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 22 (0.260) | 36 (0.490) | 28/228 | NT | 58.4% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 32 (0.440) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 152 (1.890) | 100/252 | 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 | 4037399 = | NA (NA) | 9 (0.110) | 3/256 | NT | 75.3% | intergenic (+64/‑120) | alaT/rrlA | tRNA‑Ala/23S ribosomal RNA of rrnA operon |
| ? | NC_000913 | 4209883 = | 3 (0.040) | intergenic (+34/‑160) | gltV/rrlE | tRNA‑Glu/23S ribosomal RNA of rrnE operon | |||||