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 | 52,517 | T→C | 23.5% | E757E (GAA→GAG) | imp ← | exported protein required for envelope biosynthesis and integrity |
| RA | 91,462 | T→C | 23.1% | S56P (TCT→CCT) | lpxC → | UDP‑3‑O‑acyl N‑acetylglucosamine deacetylase |
| RA | 138,172 | A→G | 13.5% | N665N (AAT→AAC) | htrE ← | predicted outer membrane usher protein |
| RA | 144,272 | C→A | 38.4% | G194V (GGC→GTC) | yadB ← | glutamyl‑Q tRNA(Asp) synthetase |
| RA | 158,183 | A→G | 28.2% | N41S (AAC→AGC) | dgt → | deoxyguanosine triphosphate triphosphohydrolase |
| RA | 163,666 | C→T | 25.9% | E77K (GAA→AAA) | yaeI ← | predicted phosphatase |
| RA | 195,616 | C→T | 36.4% | L71L (CTG→CTA) | yaeF ← | predicted lipoprotein |
| RA | 204,556 | A→G | 100% | intergenic (+156/‑28) | alaV → / → rrlH | tRNA‑Ala/23S ribosomal RNA |
| RA | 216,053 | T→C | 11.6% | intergenic (+222/‑106) | aspV → / → yafT | tRNA‑Asp/predicted aminopeptidase |
| RA | 297,667 | C→T | 26.7% | R110C (CGT→TGT) | mdlA → | fused predicted multidrug transporter subunits and ATP‑binding components of ABC superfamily |
| RA | 298,537 | C→T | 27.9% | L400L (CTG→TTG) | mdlA → | fused predicted multidrug transporter subunits and ATP‑binding components of ABC superfamily |
| RA | 300,220 | G→A | 25.0% | L372L (CTG→CTA) | mdlB → | fused predicted multidrug transporter subunits and ATP binding components of ABC superfamily |
| RA | 335,162 | G→A | 32.0% | G130G (GGC→GGT) | ybaK ← | conserved hypothetical protein |
| RA | 374,214 | G→A | 25.0% | G355D (GGT→GAT) | fepE → | regulator of length of O‑antigen component of lipopolysaccharide chains |
| RA | 397,141 | C→T | 12.1% | K216K (AAG→AAA) | lipA ← | lipoate synthase |
| RA | 498,441 | C→T | 26.6% | G24S (GGT→AGT) | galE ← | UDP‑galactose‑4‑epimerase |
| RA | 507,425 | C→A | 16.3% | A71D (GCT→GAT) | ybhH → | conserved hypothetical protein |
| RA | 558,918 | T→C | 28.0% | P55P (CCT→CCC) | cmr → | multidrug efflux system protein |
| RA | 575,416 | T→C | 36.4% | N135S (AAT→AGT) | ybjX ← | conserved hypothetical protein |
| RA | 597,552 | C→T | 19.7% | intergenic (+133/‑106) | serS → / → dmsA | seryl‑tRNA synthetase, also charges selenocysteinyl‑tRNA with serine/dimethyl sulfoxide reductase, anaerobic, subunit A |
| RA | 598,845 | C→T | 15.1% | I396I (ATC→ATT) | dmsA → | dimethyl sulfoxide reductase, anaerobic, subunit A |
| RA | 623,375 | C→T | 20.0% | T19I (ACC→ATC) | msbA → | fused lipid transporter subunits and membrane component and ATP‑binding component of ABC superfamily |
| RA | 656,044 | T→C | 26.5% | F44L (TTC→CTC) | ycbS → | predicted outer membrane usher protein |
| RA | 668,428 | C→A | 24.9% | T589K (ACG→AAG) | uup → | fused predicted transporter subunits and ATP‑binding components of ABC superfamily |
| RA | 696,779 | C→T | 26.3% | P262L (CCC→CTC) | appB → | cytochrome bd‑II oxidase, subunit II |
| RA | 782,109 | T→C | 20.9% | Q167R (CAG→CGG) | hlyE ← | hemolysin E |
| RA | 798,949 | C→T | 24.4% | M214I (ATG→ATA) | treA ← | periplasmic trehalase |
| RA | 813,910 | A→G | 26.0% | C60C (TGT→TGC) | prsA ← | phosphoribosylpyrophosphate synthase |
| RA | 899,197 | C→T | 41.2% | P78L (CCT→CTT) | pspC → | transcriptional activator |
| RA | 909,573 | C→T | 39.5% | L584L (CTG→TTG) | ycjT → | predicted hydrolase |
| RA | 1,000,186 | G→A | 43.6% | G179D (GGT→GAT) | ydgD → | predicted peptidase |
| RA | 1,011,234 | A→G | 22.7% | H221R (CAC→CGC) | rstB → | sensory histidine kinase in two‑component regulatory system with RstA |
| RA | 1,026,348 | T→C | 33.3% | E175G (GAG→GGG) | malI ← | DNA‑binding transcriptional repressor |
| RA | 1,027,446 | A→G | 30.8% | N134S (AAC→AGC) | malX → | fused maltose and glucose‑specific PTS enzyme IIBC components |
| RA | 1,036,505 | G→A | 100% | A632A (GCG→GCA) | rsxC → | fused predicted 4Fe‑4S ferredoxin‑type protein |
| RA | 1,073,671 | C→T | 41.9% | G50S (GGC→AGC) | ydhQ ← | conserved hypothetical protein |
| RA | 1,081,858 | T→C | 27.3% | N104S (AAC→AGC) | ydhY ← | predicted 4Fe‑4S ferridoxin‑type protein |
| RA | 1,094,567 | T→C | 29.2% | I604V (ATT→GTT) | ydiJ ← | predicted FAD‑linked oxidoreductase |
| RA | 1,097,909 | T→C | 37.5% | intergenic (+32/‑397) | ydiK → / → ydiL | predicted inner membrane protein/conserved hypothetical protein |
| RA | 1,099,149 | A→G | 35.3% | T130A (ACA→GCA) | ydiM → | predicted transporter |
| RA | 1,111,527 | G→A | 16.7% | C287Y (TGT→TAT) | ydiD → | short chain acyl‑CoA synthetase, anaerobic |
| RA | 1,132,803 | G→A | 28.8% | intergenic (+119/‑38) | arpB → / → yniD | ECK1718:JW5278+JW1710:b4494; hypothetical protein/hypothetical protein |
| RA | 1,142,011 | T→C | 26.2% | F152L (TTC→CTC) | katE → | hydroperoxidase HPII(III) |
| RA | 1,142,959 | A→G | 19.0% | N468D (AAC→GAC) | katE → | hydroperoxidase HPII(III) |
| RA | 1,151,211 | A→G | 22.2% | V2V (GTA→GTG) | ydjQ → | endonuclease of nucleotide excision repair |
| RA | 1,215,064 | G→A | 20.1% | L291L (CTG→CTA) | yebQ → | predicted transporter |
| RA | 1,224,676 | T→C | 15.5% | F180L (TTT→CTT) | yebU → | predicted methyltransferase |
| RA | 1,231,014 | C→T | 23.1% | G581D (GGT→GAT) | ptrB ← | protease II |
| RA | 1,249,224 | C→T | 27.8% | D17N (GAT→AAT) | ruvB ← | ATP‑dependent DNA helicase, component of RuvABC resolvasome |
| RA | 1,252,050 | T→C | 26.9% | K6K (AAA→AAG) | yebC ← | conserved hypothetical protein |
| RA | 1,253,716 | C→T | 34.1% | A241A (GCG→GCA) | aspS ← | aspartyl‑tRNA synthetase |
| RA | 1,257,376 | T→C | 26.9% | F7L (TTT→CTT) | yecP → | predicted methyltransferase |
| RA | 1,260,748 | G→A | 9.7% | S59L (TCA→TTA) | torZ ← | trimethylamine N‑oxide reductase system III, catalytic subunit |
| RA | 1,291,126 | G→A | 16.3% | intergenic (+241/+212) | yeeN → / ← asnW | conserved hypothetical protein/tRNA‑Asn |
| RA | 1,325,522 | T→G | 21.2% | K71T (AAA→ACA) | wcaL ← | predicted glycosyl transferase |
| RA | 1,330,586 | A→G | 18.2% | Y334H (TAC→CAC) | cpsG ← | phosphomannomutase |
| RA | 1,352,427 | T→C | 25.6% | N101D (AAC→GAC) | thiD ← | bifunctional hydroxy‑methylpyrimidine kinase and hydroxy‑phosphomethylpyrimidine kinase |
| RA | 1,418,334 | G→A | 23.8% | V95I (GTC→ATC) | narP → | DNA‑binding response regulator in two‑component regulatory system with NarQ or NarX |
| RA | 1,439,412 | G→A | 27.9% | A297V (GCT→GTT) | ompC ← | outer membrane porin protein C |
| RA | 1,475,665 | A→T | 20.7% | T244S (ACC→TCC) | nrdB → | ribonucleoside diphosphate reductase 1, beta subunit, ferritin‑like |
| RA | 1,485,005 | C→T | 13.1% | D279N (GAT→AAT) | menF ← | isochorismate synthase 2 |
| RA | 1,496,561 | C→T | 57.6% | M327I (ATG→ATA) | nuoF ← | NADH:ubiquinone oxidoreductase, chain F |
| RA | 1,509,579 | G→A | 30.9% | A42T (GCA→ACA) | ackA → | acetate kinase A and propionate kinase 2 |
| RA | 1,511,849 | T→C | 58.5% | W373R (TGG→CGG) | pta → | phosphate acetyltransferase |
| RA | 1,523,433 | G→T | 24.9% | A78S (GCC→TCC) | flk → | predicted flagella assembly protein |
| RA | 1,523,658 | C→T | 48.6% | Q153* (CAA→TAA) | flk → | predicted flagella assembly protein |
| RA | 1,533,542 | G→A | 29.4% | P51S (CCT→TCT) | prmB ← | N5‑glutamine methyltransferase |
| RA | 1,572,316 | T→C | 9.3% | *472* (TAA→TGA) | gltX ← | glutamyl‑tRNA synthetase |
| RA | 1,581,504 | C→T | 9.1% | L577L (TTG→TTA) | ligA ← | DNA ligase, NAD(+)‑dependent |
| RA | 1,591,415 | G→T | 42.3% | K203N (AAG→AAT) | yfeS → | conserved hypothetical protein |
| RA | 1,598,488 | C→T | 32.6% | A60A (GCG→GCA) | yfeT ← | predicted DNA‑binding transcriptional regulator |
| RA | 1,643,860 | A→G | 26.8% | R9R (CGT→CGC) | purC ← | phosphoribosylaminoimidazole‑succinocarboxamide synthetase |
| RA | 1,664,529 | G→A | 36.4% | I231I (ATC→ATT) | guaA ← | GMP synthetase |
| RA | 1,680,754 | T→C | 31.8% | Y1407C (TAC→TGC) | yfhM ← | conserved hypothetical protein |
| RA | 1,695,295 | G→A | 37.9% | Q239* (CAG→TAG) | yfhQ ← | predicted methyltransferase |
| RA | 1,697,632 | A→G | 17.6% | Y195C (TAT→TGT) | yfhR → | predicted peptidase |
| RA | 1,700,462 | A→G | 31.5% | L24P (CTA→CCA) | hcaT ← | predicted 3‑phenylpropionic transporter |
| RA | 1,763,556 | T→C | 35.5% | noncoding (288/1542 nt) | rrsG ← | 16S ribosomal RNA |
| RA | 1,763,636 | A→G | 21.0% | noncoding (208/1542 nt) | rrsG ← | 16S ribosomal RNA |
| RA | 1,784,184 | T→C | 22.6% | I223T (ATA→ACA) | yfjB → | NAD kinase |
| RA | 1,789,346 | Δ1 bp | 34.3% | coding (483/1269 nt) | ygaF → | hypothetical protein |
| RA | 1,798,695 | A→G | 11.5% | Q239R (CAA→CGA) | proV → | glycine betaine transporter subunit |
| RA | 1,803,598 | T→C | 12.5% | N30N (AAT→AAC) | ygaH → | predicted inner membrane protein |
| RA | 1,807,377 | T→C | 6.4% | intergenic (+58/+6) | emrB → / ← luxS | multidrug efflux system protein/S‑ribosylhomocysteinase |
| RA | 1,827,932 | C→T | 34.1% | A392V (GCG→GTG) | mutS → | methyl‑directed mismatch repair protein |
| RA | 1,833,531 | C→T | 41.3% | R92C (CGC→TGC) | ygbL → | predicted class II aldolase |
| RA | 1,834,094 | A→G | 13.9% | D65G (GAT→GGT) | ygbM → | conserved hypothetical protein |
| RA | 1,867,615 | G→A | 37.3% | T429I (ACC→ATC) | ygcU ← | predicted FAD containing dehydrogenase |
| RA | 1,874,329 | A→G | 14.1% | I191T (ATT→ACT) | ygcF ← | conserved hypothetical protein |
| RA | 1,883,198 | A→G | 22.5% | F429L (TTC→CTC) | rumA ← | 23S rRNA (uracil‑5)‑methyltransferase |
| RA | 1,890,961 | G→A | 14.3% | P208S (CCG→TCG) | gudP ← | predicted D‑glucarate transporter |
| RA | 1,892,019:1 | +GC | 100% | intergenic (‑437/+54) | gudP ← / ← ygdL | predicted D‑glucarate transporter/conserved hypothetical protein |
| RA | 1,914,848 | T→C | 28.0% | E208E (GAA→GAG) | ptsP ← | fused PEP‑protein phosphotransferase (enzyme I) of PTS system |
| RA | 1,975,134 | A→G | 7.4% | intergenic (+280/‑144) | metK → / → galP | methionine adenosyltransferase 1/D‑galactose transporter |
| RA | 1,993,572 | G→A | 24.5% | V289M (GTG→ATG) | nupG → | nucleoside transporter |
| RA | 2,004,302 | G→A | 25.0% | S483F (TCT→TTT) | hybC ← | hydrogenase 2, large subunit |
| RA | 2,144,345 | G→A | 13.3% | D206N (GAT→AAT) | argG → | argininosuccinate synthetase |
| RA | 2,187,308 | T→C | 34.6% | P183P (CCA→CCG) | nanT ← | sialic acid transporter |
| RA | 2,211,683 | A→G | 18.6% | I465I (ATT→ATC) | rng ← | ribonuclease G |
| RA | 2,236,903 | G→A | 31.4% | A150T (GCT→ACT) | purD → | phosphoribosylglycinamide synthetase phosphoribosylamine‑glycine ligase |
| RA | 2,269,809 | T→C | 9.4% | V174V (GTA→GTG) | murB ← | UDP‑N‑acetylenolpyruvoylglucosamine reductase, FAD‑binding |
| RA | 2,283,783 | G→T | 14.2% | L39M (CTG→ATG) | oxyR ← | DNA‑binding transcriptional dual regulator |
| RA | 2,321,698 | G→A | 13.4% | T93I (ACC→ATC) | cdh ← | CDP‑diacylglycerol phosphotidylhydrolase |
| RA | 2,359,867 | G→A | 42.7% | noncoding (1228/2905 nt) | rrlA ← | 23S ribosomal RNA |
| RA | 2,359,876 | C→T | 38.5% | noncoding (1219/2905 nt) | rrlA ← | 23S ribosomal RNA |
| RA | 2,364,103 | A→G | 30.6% | W456R (TGG→CGG) | trkH ← | potassium transporter |
| RA | 2,371,447 | A→G | 48.6% | F214L (TTT→CTT) | fre ← | flavin reductase |
| RA | 2,377,802 | A→T | 20.0% | Y196N (TAC→AAC) | ubiB ← | 2‑octaprenylphenol hydroxylase |
| RA | 2,450,298 | A→G | 22.2% | W78R (TGG→CGG) | yifE ← | conserved hypothetical protein |
| RA | 2,467,238 | G→T | 16.6% | L234L (CTG→CTT) | atpA → | F1 sector of membrane‑bound ATP synthase, alpha subunit |
| RA | 2,473,718 | C→T | 25.9% | F331F (TTC→TTT) | glmS → | L‑glutamine:D‑fructose‑6‑phosphate aminotransferase |
| RA | 2,482,022 | G→A | 8.9% | A281V (GCG→GTG) | mdtL ← | multidrug efflux system protein |
| RA | 2,516,656 | C→T | 31.7% | A102T (GCT→ACT) | trmH ← | tRNA (Guanosine‑2'‑O‑)‑methyltransferase |
| RA | 2,523,040 | T→C | 31.3% | K225K (AAA→AAG) | dinD ← | DNA‑damage‑inducible protein |
| RA | 2,528,498 | C→T | 21.8% | D83N (GAT→AAT) | dfp ← | fused 4'‑phosphopantothenoylcysteine decarboxylase and phosphopantothenoylcysteine synthetase, FMN‑binding |
| RA | 2,530,398 | G→A | 11.1% | A26T (GCA→ACA) | mutM → | formamidopyrimidine/5‑formyluracil/ 5‑hydroxymethyluracil DNA glycosylase |
| RA | 2,531,609 | A→G | 7.3% | I14I (ATT→ATC) | coaD ← | pantetheine‑phosphate adenylyltransferase |
| RA | 2,540,373 | G→T | 8.1% | D300Y (GAT→TAT) | rfaJ → | UDP‑D‑glucose:(galactosyl)lipopolysaccharide glucosyltransferase |
| RA | 2,597,495 | A→G | 6.0% | intergenic (‑491/+386) | arsR ← / ← gor | DNA‑binding transcriptional regulator/glutathione oxidoreductase |
| RA | 2,605,272 | A→G | 31.5% | L50L (CTT→CTC) | uspA ← | universal stress global response regulator |
| RA | 2,632,970 | A→G | 55.6% | K421R (AAA→AGA) | livM → | leucine/isoleucine/valine transporter subunit |
| RA | 2,639,808 | A→G | 20.6% | T245A (ACG→GCG) *147Q (TAA→CAA) |
ugpQ → yhhA ← |
glycerophosphodiester phosphodiesterase, cytosolic conserved hypothetical protein |
| RA | 2,651,936 | C→T | 15.1% | A57V (GCG→GTG) | glgC → | glucose‑1‑phosphate adenylyltransferase |
| RA | 2,677,626 | C→T | 16.7% | A102T (GCA→ACA) | yhgA ← | predicted transposase |
| RA | 2,681,918 | A→G | 25.0% | R598R (CGT→CGC) | yhgF ← | predicted transcriptional accessory protein |
| RA | 2,683,278 | T→G | 13.2% | Y145S (TAT→TCT) | yhgF ← | predicted transcriptional accessory protein |
| RA | 2,703,672 | G→A | 33.3% | A355T (GCC→ACC) | aroB → | 3‑dehydroquinate synthase |
| RA | 2,726,174 | G→A | 35.7% | R303R (CGC→CGT) | yheS ← | fused predicted transporter subunits and ATP‑binding components of ABC superfamily |
| RA | 2,732,642 | C→A | 26.6% | Q238K (CAA→AAA) | yheO → | predicted DNA‑binding transcriptional regulator |
| RA | 2,802,519 | T→A | 56.7% | D196V (GAT→GTT) | qor ← | quinone oxidoreductase, NADPH‑dependent |
| RA | 2,850,177 | G→A | 26.9% | Q286* (CAG→TAG) | yjeP ← | predicted mechanosensitive channel |
| RA | 2,858,845 | G→A | 41.3% | S373S (TCG→TCA) | amiB → | N‑acetylmuramoyl‑l‑alanine amidase II |
| RA | 2,864,584 | C→T | 24.1% | A295A (GCC→GCT) | hflK → | modulator for HflB protease specific for phage lambda cII repressor |
| RA | 2,912,429 | C→T | 23.9% | A135T (GCG→ACG) | pyrI ← | aspartate carbamoyltransferase, regulatory subunit |
| RA | 2,937,934 | T→C | 6.6% | intergenic (+61/‑208) | leuX → / → yjhV | tRNA‑Leu/hypothetical protein |
| RA | 2,947,335 | A→G | 17.8% | L158P (CTG→CCG) | dnaT ← | DNA biosynthesis protein |
| RA | 2,948,123 | T→C | 27.5% | T40A (ACC→GCC) | yjjB ← | conserved inner membrane protein |
| RA | 2,971,396 | T→C | 13.9% | V71A (GTG→GCG) | serB → | 3‑phosphoserine phosphatase |
| RA | 2,986,542 | A→G | 19.9% | L19L (TTG→CTG) | arcA ← | DNA‑binding response regulator in two‑component regulatory system with ArcB or CpxA |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | minE | 251998 | 252034 | 37 | 5 [4] | [3] 5 | malZ | maltodextrin glucosidase |
| * | * | ÷ | minE | 444400 | 444423 | 24 | 5 [3] | [4] 6 | kdpE | DNA‑binding response regulator in two‑component regulatory system with KdpD |
| * | * | ÷ | minE | 865549 | 865585 | 37 | 5 [3] | [4] 5 | yciQ | predicted inner membrane protein |
| * | * | ÷ | minE | 899408 | 899471 | 64 | 5 [4] | [4] 6 | pspD | peripheral inner membrane phage‑shock protein |
| * | * | ÷ | minE | 1154064 | 1154099 | 36 | 5 [2] | [4] 6 | astE | succinylglutamate desuccinylase |
| * | * | ÷ | minE | 1616708 | 1616752 | 45 | 5 [3] | [4] 5 | eutE | predicted aldehyde dehydrogenase, ethanolamine utilization protein |
| * | * | ÷ | minE | 1847624 | 1847689 | 66 | 5 [4] | [4] 5 | iap/ygbF | aminopeptidase in alkaline phosphatase isozyme conversion/hypothetical protein |