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 | 70,918 | C→T | 6.9% | R178W (CGG→TGG) | araC → | ara regulon transcriptional activator; autorepressor |
| RA | 78,170 | A→T | 5.6% | S184C (AGT→TGT) | setA → | broad specificity sugar efflux system |
| RA | 78,187 | A→G | 5.9% | A189A (GCA→GCG) | setA → | broad specificity sugar efflux system |
| RA | 164,557 | G→C | 5.6% | intergenic (+23/‑173) | hrpB → / → mrcB | putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase |
| RA | 164,558 | T→A | 5.6% | intergenic (+24/‑172) | hrpB → / → mrcB | putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase |
| RA | 207,586 | T→C | 6.2% | Y821H (TAC→CAC) | dnaE → | DNA polymerase III alpha subunit |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 324,581 | C→T | 5.5% | intergenic (+128/+115) | ykgG → / ← ykgH | LutC family protein; putative electron transport chain YkgEFG component/putative inner membrane protein |
| RA | 330,555 | T→C | 6.1% | W365R (TGG→CGG) | betT → | choline transporter of high affinity |
| RA | 364,607 | A→T | 7.4% | F567I (TTC→ATC) | lacZ ← | beta‑D‑galactosidase |
| RA | 494,528 | C→T | 6.4% | R42C (CGT→TGT) | recR → | gap repair protein |
| RA | 510,362 | C→T | 5.9% | E340K (GAA→AAA) | copA ← | copper transporter |
| RA | 530,694 | G→A | 6.3% | A178V (GCG→GTG) | mnmH ← | tRNA 2‑selenouridine synthase, selenophosphate‑dependent |
| RA | 542,182 | G→A | 6.2% | V99I (GTC→ATC) | glxK → | glycerate kinase II |
| RA | 560,670 | C→T | 5.2% | P325L (CCG→CTG) | sfmD → | putative outer membrane export usher protein |
| RA | 573,037 | C→T | 5.1% | A39A (GCC→GCT) | ninE → | DLP12 prophage; conserved protein |
| RA | 615,932 | A→G | 6.1% | S592S (TCA→TCG) | entF → | enterobactin synthase multienzyme complex component, ATP‑dependent |
| RA | 616,669 | C→T | 6.2% | T838I (ACC→ATC) | entF → | enterobactin synthase multienzyme complex component, ATP‑dependent |
| RA | 663,973 | T→C | 5.9% | intergenic (‑10/+129) | dacA ← / ← rlpA | D‑alanyl‑D‑alanine carboxypeptidase (penicillin‑binding protein 5)/septal ring protein, suppressor of prc, minor lipoprotein |
| RA | 672,098 | G→A | 6.1% | P30L (CCT→CTT) | lptE ← | LPS assembly OM complex LptDE, lipoprotein component |
| RA | 721,865 | T→A | 6.8% | A850A (GCA→GCT) | kdpD ← | fused sensory histidine kinase in two‑component regulatory system with KdpE: signal sensing protein |
| RA | 724,846 | T→A | 6.2% | E45V (GAA→GTA) | kdpC ← | potassium translocating ATPase, subunit C |
| RA | 767,560 | C→T | 7.3% | A526V (GCA→GTA) | mngA → | fused 2‑O‑a‑mannosyl‑D‑glycerate specific PTS enzymes: IIA component/IIB component/IIC component |
| RA | 814,856 | C→T | 9.1% | A444V (GCA→GTA) | uvrB → | exision nuclease of nucleotide excision repair, DNA damage recognition component |
| RA | 868,920 | T→A | 5.4% | G467G (GGT→GGA) | gsiA → | glutathione ABC transporter ATPase |
| RA | 886,947 | A→G | 5.1% | V131V (GTT→GTC) | ybjJ ← | putative drug efflux MFS transporter, inner membrane protein |
| RA | 907,330 | C→T | 5.8% | R318Q (CGA→CAA) | ybjT ← | putative NAD‑dependent oxidoreductase |
| RA | 927,053 | C→T | 6.6% | G127D (GGC→GAC) | aat ← | leucyl/phenylalanyl‑tRNA‑protein transferase |
| RA | 963,086 | C→T | 6.7% | G364G (GGC→GGT) | rpsA → | 30S ribosomal subunit protein S1 |
| RA | 1,077,193 | T→C | 7.1% | T564A (ACC→GCC) | putA ← | fused DNA‑binding transcriptional regulator/proline dehydrogenase/pyrroline‑5‑carboxylate dehydrogenase |
| RA | 1,139,225 | T→C | 5.1% | I283T (ATT→ACT) | flgK → | flagellar hook‑filament junction protein 1 |
| RA | 1,147,690 | G→A | 8.6% | A24T (GCA→ACA) ‡ | plsX → | putative phosphate acyltransferase |
| RA | 1,147,691 | C→T | 8.7% | A24V (GCA→GTA) ‡ | plsX → | putative phosphate acyltransferase |
| RA | 1,147,692 | A→G | 8.6% | A24A (GCA→GCG) ‡ | plsX → | putative phosphate acyltransferase |
| RA | 1,147,693 | T→C | 8.1% | L25L (TTG→CTG) | plsX → | putative phosphate acyltransferase |
| RA | 1,192,500 | A→G | 6.5% | I44I (ATT→ATC) | hflD ← | putative lysogenization regulator |
| RA | 1,217,722 | C→A | 5.8% | P132H (CCT→CAT) | ycgG → | putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase |
| RA | 1,233,710 | A→G | 6.1% | G336G (GGT→GGC) | nhaB ← | sodium:proton antiporter |
| RA | 1,287,024 | G→A | 8.7% | intergenic (+498/+42) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| RA | 1,342,315 | G→A | 6.1% | S132N (AGC→AAC) | pyrF → | orotidine‑5'‑phosphate decarboxylase |
| RA | 1,349,850 | C→T | 6.8% | L86L (TTG→TTA) | yciW ← | putative oxidoreductase |
| RA | 1,402,942 | T→A | 5.7% | N105I (AAT→ATT) | abgB ← | p‑aminobenzoyl‑glutamate hydrolase, B subunit |
| RA | 1,449,801 | T→C | 6.2% | T517A (ACG→GCG) | tynA ← | tyramine oxidase, copper‑requiring |
| RA | 1,493,798 | G→A | 5.8% | V443V (GTG→GTA) | trg → | methyl‑accepting chemotaxis protein III, ribose and galactose sensor receptor |
| RA | 1,525,378 | G→A | 9.1% | N201N (AAC→AAT) | ansP ← | L‑asparagine transporter |
| RA | 1,548,986 | C→T | 5.9% | P529L (CCG→CTG) | fdnG → | formate dehydrogenase‑N, alpha subunit, nitrate‑inducible |
| RA | 1,587,825 | C→A | 9.6% | A158S (GCG→TCG) | ydeR ← | putative fimbrial‑like adhesin protein |
| RA | 1,591,287 | T→C | 5.3% | K297R (AAA→AGA) | hipA ← | inactivating GltX kinase facilitating persister formation; toxin of HipAB TA pair; autokinase |
| RA | 1,635,808 | C→T | 5.2% | A14T (GCA→ACA) | stfQ ← | Qin prophage; putative side tail fibre assembly protein |
| RA | 1,683,685 | C→A | 6.1% | L268L (CTC→CTA) | rstB → | sensory histidine kinase of RstAB two‑component system |
| RA | 1,700,606 | G→A | 6.0% | A418T (GCT→ACT) | malX → | maltose and glucose‑specific PTS enzyme IIB component and IIC component |
| RA | 1,724,105 | C→T | 6.6% | A662V (GCA→GTA) | ydhK → | putative efflux protein (PET) component of YdhJK efflux pump |
| RA | 1,845,795 | C→A | 5.5% | R389L (CGG→CTG) | topB ← | DNA topoisomerase III |
| RA | 1,903,717 | C→T | 6.9% | L212L (CTC→CTT) | manY → | mannose‑specific enzyme IIC component of PTS |
| RA | 1,939,871 | G→A | 5.3% | P108L (CCG→CTG) | lpxM ← | myristoyl‑acyl carrier protein (ACP)‑dependent acyltransferase |
| RA | 1,947,435 | A→T | 6.1% | S239S (TCT→TCA) | yebC ← | UPF0082 family protein |
| RA | 1,956,702 | C→T | 5.4% | A102A (GCG→GCA) | torZ ← | trimethylamine N‑oxide reductase system III, catalytic subunit |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| RA | 2,070,150 | T→C | 44.5% | R11G (AGA→GGA) | insC1 ← | IS2 repressor TnpA |
| RA | 2,100,923 | A→G | 100% | S116P (TCA→CCA) | gnd ← | 6‑phosphogluconate dehydrogenase, decarboxylating |
| RA | 2,128,084 | T→C | 5.5% | E77E (GAA→GAG) | gmd ← | GDP‑D‑mannose dehydratase, NAD(P)‑binding |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,141,323 | T→C | 6.9% | H97R (CAT→CGT) | asmA ← | suppressor of OmpF assembly mutants; putative outer membrane protein assembly factor; inner membrane‑anchored periplasmic protein |
| RA | 2,156,030 | C→T | 6.1% | A256A (GCC→GCT) | mdtB → | multidrug efflux system, subunit B |
| 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 | 2,187,133 | G→A | 6.0% | M58I (ATG→ATA) | rcnB → | periplasmic modulator of Ni and Co efflux |
| RA | 2,241,524 | C→T | 6.1% | A49T (GCC→ACC) | galS ← | galactose‑ and fucose‑inducible galactose regulon transcriptional isorepressor; mgl operon transcriptional repressor; autorepressor |
| RA | 2,248,744 | G→A | 6.1% | P292L (CCG→CTG) | yeiE ← | putative DNA‑binding transcriptional regulator |
| RA | 2,306,444 | T→A | 5.3% | K104I (AAA→ATA) | mqo ← | malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,351,872 | C→T | 8.0% | G168D (GGT→GAT) | glpT ← | sn‑glycerol‑3‑phosphate transporter |
| RA | 2,357,836 | G→A | 8.5% | pseudogene (33/198 nt) | ypaA → | pseudogene, C‑terminal fragment, Transposase_31 family |
| RA | 2,439,269 | G→C | 6.2% | V284V (GTC→GTG) | yfcJ ← | putative arabinose efflux transporter |
| RA | 2,492,677 | C→T | 6.4% | G193E (GGG→GAG) | frc ← | formyl‑CoA transferase, NAD(P)‑binding |
| RA | 2,556,516 | Δ1 bp | 6.8% | coding (782/888 nt) | eutC ← | ethanolamine ammonia‑lyase, small subunit (light chain) |
| RA | 2,560,985 | C→A | 18.5% | intergenic (+87/‑383) | yffL → / → yffM | CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein |
| RA | 2,574,070 | C→T | 5.0% | C79Y (TGC→TAC) | eutT ← | cobalamin adenosyltransferase involved in ethanolamine utilization |
| RA | 2,611,356 | C→T | 5.5% | D217D (GAC→GAT) | hyfI → | hydrogenase 4, Fe‑S subunit |
| RA | 2,680,316 | C→T | 5.3% | P810P (CCG→CCA) | yphG ← | DUF4380 domain‑containing TPR repeat protein |
| RA | 2,684,906 | A→T | 5.2% | M201K (ATG→AAG) | glyA ← | serine hydroxymethyltransferase |
| RA | 2,722,988 | G→T | 6.0% | D88Y (GAC→TAC) | pssA → | phosphatidylserine synthase; CDP‑diacylglycerol‑serine O‑phosphatidyltransferase |
| RA | 2,776,881 | G→A | 5.4% | R2K (AGA→AAA) | ypjJ → | uncharacterized protein |
| RA | 2,868,951 | A→G | 5.3% | I190T (ATT→ACT) | pcm ← | L‑isoaspartate protein carboxylmethyltransferase type II |
| RA | 2,869,858 | A→G | 5.1% | C139C (TGT→TGC) | umpG ← | broad specificity 5'(3')‑nucleotidase and polyphosphatase |
| RA | 2,891,288 | G→A | 5.9% | A204V (GCG→GTG) | cysJ ← | sulfite reductase, alpha subunit, flavoprotein |
| RA | 2,953,953 | A→T | 6.3% | L684H (CTT→CAT) | recB ← | exonuclease V (RecBCD complex), beta subunit |
| RA | 3,010,797 | A→T | 5.2% | Q257L (CAG→CTG) | hyuA → | D‑stereospecific phenylhydantoinase |
| RA | 3,067,393 | A→G | 5.1% | F230L (TTC→CTC) | yggE ← | oxidative stress defense protein |
| RA | 3,095,489 | Δ1 bp | 5.7% | coding (392/705 nt) | yggS → | UPF0001 family protein, PLP‑binding |
| RA | 3,142,784 | G→T | 5.6% | A69E (GCG→GAG) | hybC ← | hydrogenase 2, large subunit |
| RA | 3,142,835 | T→C | 5.2% | D52G (GAT→GGT) | hybC ← | hydrogenase 2, large subunit |
| RA | 3,254,732 | C→G | 6.0% | G138G (GGC→GGG) | yhaK → | redox‑sensitive bicupin |
| RA | 3,311,107 | C→G | 5.5% | G21A (GGC→GCC) | pnp ← | polynucleotide phosphorylase/polyadenylase |
| RA | 3,362,934 | C→A | 14.2% | P43H (CCT→CAT) | yhcD → | putative outer membrane fimbrial subunit usher protein |
| RA | 3,362,956 | C→A | 13.2% | S50S (TCC→TCA) | yhcD → | putative outer membrane fimbrial subunit usher protein |
| RA | 3,454,209 | T→C | 5.3% | E397G (GAA→GGA) | gspA ← | general secretory pathway component, cryptic |
| 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 | 3,560,815 | A→G | 7.0% | L213P (CTA→CCA) | glpG ← | rhomboid intramembrane serine protease |
| RA | 3,690,773 | T→C | 6.0% | K612R (AAA→AGA) | bcsB ← | regulator of cellulose synthase, cyclic di‑GMP binding |
| RA | 3,725,949 | G→A | 5.1% | M21I (ATG→ATA) | wecH → | O‑acetyltransferase for enterobacterial common antigen (ECA) |
| RA | 3,734,215 | A→G | 6.8% | S166G (AGC→GGC) | xylH → | D‑xylose ABC transporter permease |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,852,061 | T→C | 6.4% | M242V (ATG→GTG) | ilvB ← | acetolactate synthase 2 large subunit |
| JC JC | 3,906,168 | IS5 (+) +4 bp | 100% | coding (397‑400/837 nt) | bglG ← | transcriptional antiterminator of the bgl operon |
| RA | 3,946,233 | A→G | 8.6% | noncoding (2530/2904 nt) | rrlC → | 23S ribosomal RNA of rrnC operon |
| RA | 3,949,413 | A→G | 5.4% | L186P (CTA→CCA) | yifB ← | magnesium chelatase family protein and putative transcriptional regulator |
| JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,213,789 | T→C | 5.6% | Q112R (CAG→CGG) | yjaB ← | GNAT‑family putative N‑acetyltransferase; acetyl coenzyme A‑binding protein |
| RA | 4,296,060 | C→T | 27.0% | 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 | 4,447,423 | T→C | 5.9% | A1104A (GCT→GCC) | tamB → | translocation and assembly module for autotransporter export, inner membrane subunit |
| RA | 4,520,018 | G→A | 5.4% | R103W (CGG→TGG) | yjhU ← | putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element |
| JC JC | 4,620,780 | IS1 (–) +9 bp | 100% | coding (1178‑1186/1224 nt) | deoB → | phosphopentomutase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1299499–1300693 | 1300693 | 1–1195 | 147 [0] | [0] 151 | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| * | * | ÷ | NC_000913 | 3423760–3424234 | 3424544–3424238 | 5–785 | 27 [24] | [26] 29 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3514391 | 3515081 | 691 | 27 [22] | [25] 29 | [rpe]–[dam] | [rpe],[dam] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 888271 = | 65 (0.770) | 3 (0.040) | 3/238 | NT | 5.3% | coding (1549/1686 nt) | ybjL | putative transporter |
| ? | NC_000913 | 888316 = | 46 (0.570) | coding (1504/1686 nt) | ybjL | putative transporter | |||||
| * | ? | NC_000913 | 1207790 = | 35 (0.410) | 38 (0.520) | 33/218 | NT | 52.2% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 39 (0.530) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 35 (0.410) | 44 (0.600) | 36/218 | NT | 55.9% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 39 (0.530) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 125 (1.640) | 88/226 | NT | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | = 1300693 | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 1299499 = | NA (NA) | 124 (1.630) | 84/226 | NT | 100% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 1300694 = | 0 (0.000) | intergenic (+1449/‑488) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 1764796 = | 61 (0.720) | 4 (0.050) | 4/244 | NT | 6.2% | intergenic (‑16/+138) | rydB/ydiH | novel sRNA, function unknown/uncharacterized protein |
| ? | NC_000913 | 1764818 = | 61 (0.740) | intergenic (‑38/+116) | rydB/ydiH | novel sRNA, function unknown/uncharacterized protein | |||||