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 | 60,568 | G→A | 46.0% | R125R (CGC→CGT) | hepA ← | RNA polymerase‑associated helicase protein |
| RA | 80,697 | T→C | 6.8% | S436S (AGT→AGC) | murF → | UDP‑N‑acetylmuramoyl‑tripeptide:D‑alanyl‑D‑ alanine ligase |
| RA | 138,172 | A→G | 24.7% | N665N (AAT→AAC) | htrE ← | predicted outer membrane usher protein |
| RA | 158,183 | A→G | 8.9% | N41S (AAC→AGC) | dgt → | deoxyguanosine triphosphate triphosphohydrolase |
| RA | 163,666 | C→T | 29.5% | E77K (GAA→AAA) | yaeI ← | predicted phosphatase |
| RA | 199,135 | T→A | 33.8% | S207C (AGC→TGC) | metQ ← | DL‑methionine transporter subunit |
| RA | 204,556 | A→G | 100% | intergenic (+156/‑28) | alaV → / → rrlH | tRNA‑Ala/23S ribosomal RNA |
| RA | 216,053 | T→C | 23.1% | intergenic (+222/‑106) | aspV → / → yafT | tRNA‑Asp/predicted aminopeptidase |
| RA | 258,220 | C→T | 7.4% | P83S (CCG→TCG) | secF → | SecYEG protein translocase auxillary subunit |
| RA | 286,800 | T→C | 18.7% | P302P (CCT→CCC) | clpX → | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease |
| RA | 297,667 | C→T | 15.8% | R110C (CGT→TGT) | mdlA → | fused predicted multidrug transporter subunits and ATP‑binding components of ABC superfamily |
| RA | 298,537 | C→T | 38.2% | L400L (CTG→TTG) | mdlA → | fused predicted multidrug transporter subunits and ATP‑binding components of ABC superfamily |
| RA | 374,214 | G→A | 29.3% | G355D (GGT→GAT) | fepE → | regulator of length of O‑antigen component of lipopolysaccharide chains |
| RA | 402,650 | C→T | 39.6% | G38D (GGC→GAC) | rlpA ← | minor lipoprotein |
| RA | 405,935 | T→G | 36.4% | Q118P (CAG→CCG) | ybeA ← | conserved hypothetical protein |
| RA | 430,231 | G→A | 22.7% | D280N (GAC→AAC) | glnS → | glutamyl‑tRNA synthetase |
| RA | 447,412 | G→A | 58.3% | R102C (CGC→TGC) | kdpD ← | fused sensory histidine kinase in two‑component regulatory system with KdpE |
| RA | 498,441 | C→T | 44.2% | G24S (GGT→AGT) | galE ← | UDP‑galactose‑4‑epimerase |
| RA | 507,425 | C→A | 15.1% | A71D (GCT→GAT) | ybhH → | conserved hypothetical protein |
| RA | 581,876 | G→A | 27.2% | P638P (CCG→CCA) | clpA → | ATPase and specificity subunit of ClpA‑ClpP ATP‑dependent serine protease, chaperone activity |
| RA | 597,552 | C→T | 27.1% | intergenic (+133/‑106) | serS → / → dmsA | seryl‑tRNA synthetase, also charges selenocysteinyl‑tRNA with serine/dimethyl sulfoxide reductase, anaerobic, subunit A |
| RA | 623,375 | C→T | 34.0% | T19I (ACC→ATC) | msbA → | fused lipid transporter subunits and membrane component and ATP‑binding component of ABC superfamily |
| RA | 656,044 | T→C | 15.7% | F44L (TTC→CTC) | ycbS → | predicted outer membrane usher protein |
| RA | 696,779 | C→T | 32.0% | P262L (CCC→CTC) | appB → | cytochrome bd‑II oxidase, subunit II |
| RA | 813,910 | A→G | 17.9% | C60C (TGT→TGC) | prsA ← | phosphoribosylpyrophosphate synthase |
| RA | 843,375 | A→G | 8.9% | A80A (GCA→GCG) | galU → | glucose‑1‑phosphate uridylyltransferase |
| RA | 880,753 | G→A | 51.1% | intergenic (+72/‑122) | yciM → / → pyrF | conserved hypothetical protein/orotidine‑5'‑phosphate decarboxylase |
| RA | 899,197 | C→T | 20.9% | P78L (CCT→CTT) | pspC → | transcriptional activator |
| RA | 899,672 | T→C | 8.3% | L15P (CTG→CCG) | pspE → | thiosulfate:cyanide sulfurtransferase |
| RA | 909,573 | C→T | 30.6% | L584L (CTG→TTG) | ycjT → | predicted hydrolase |
| RA | 1,005,633 | C→T | 5.8% | intergenic (‑39/‑485) | pntA ← / → ydgH | pyridine nucleotide transhydrogenase, alpha subunit/hypothetical protein |
| RA | 1,011,234 | A→G | 26.9% | H221R (CAC→CGC) | rstB → | sensory histidine kinase in two‑component regulatory system with RstA |
| RA | 1,026,348 | T→C | 25.7% | E175G (GAG→GGG) | malI ← | DNA‑binding transcriptional repressor |
| RA | 1,027,446 | A→G | 20.8% | 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 | 1,069,991 | G→A | 10.2% | Q296Q (CAG→CAA) | cfa → | cyclopropane fatty acyl phospholipid synthase |
| RA | 1,073,671 | C→T | 24.4% | G50S (GGC→AGC) | ydhQ ← | conserved hypothetical protein |
| RA | 1,082,141 | C→T | 14.1% | D10N (GAT→AAT) | ydhY ← | predicted 4Fe‑4S ferridoxin‑type protein |
| RA | 1,094,567 | T→C | 33.3% | I604V (ATT→GTT) | ydiJ ← | predicted FAD‑linked oxidoreductase |
| RA | 1,111,527 | G→A | 21.6% | C287Y (TGT→TAT) | ydiD → | short chain acyl‑CoA synthetase, anaerobic |
| RA | 1,132,803 | G→A | 24.7% | intergenic (+119/‑38) | arpB → / → yniD | ECK1718:JW5278+JW1710:b4494; hypothetical protein/hypothetical protein |
| RA | 1,142,011 | T→C | 16.0% | F152L (TTC→CTC) | katE → | hydroperoxidase HPII(III) |
| RA | 1,142,959 | A→G | 43.2% | N468D (AAC→GAC) | katE → | hydroperoxidase HPII(III) |
| RA | 1,215,064 | G→A | 30.2% | L291L (CTG→CTA) | yebQ → | predicted transporter |
| RA | 1,224,676 | T→C | 25.0% | F180L (TTT→CTT) | yebU → | predicted methyltransferase |
| RA | 1,249,224 | C→T | 7.8% | D17N (GAT→AAT) | ruvB ← | ATP‑dependent DNA helicase, component of RuvABC resolvasome |
| RA | 1,257,376 | T→C | 13.0% | F7L (TTT→CTT) | yecP → | predicted methyltransferase |
| RA | 1,283,225 | C→T | 5.1% | A1668A (GCC→GCT) | yeeJ → | adhesin |
| RA | 1,291,126 | G→A | 30.1% | intergenic (+241/+212) | yeeN → / ← asnW | conserved hypothetical protein/tRNA‑Asn |
| RA | 1,328,372 | G→A | 50.0% | F131F (TTC→TTT) | wzxC ← | colanic acid exporter |
| RA | 1,408,722 | G→A | 37.1% | A331T (GCG→ACG) | yejF → | fused predicted oligopeptide transporter subunits and ATP‑binding components of ABC superfamily |
| RA | 1,418,334 | G→A | 41.8% | V95I (GTC→ATC) | narP → | DNA‑binding response regulator in two‑component regulatory system with NarQ or NarX |
| RA | 1,475,665 | A→T | 34.4% | T244S (ACC→TCC) | nrdB → | ribonucleoside diphosphate reductase 1, beta subunit, ferritin‑like |
| RA | 1,485,005 | C→T | 47.9% | D279N (GAT→AAT) | menF ← | isochorismate synthase 2 |
| RA | 1,500,488 | A→G | 10.7% | F38L (TTT→CTT) | nuoB ← | NADH:ubiquinone oxidoreductase, chain B |
| RA | 1,511,807 | G→A | 21.5% | E359K (GAG→AAG) | pta → | phosphate acetyltransferase |
| RA | 1,523,433 | G→T | 29.2% | A78S (GCC→TCC) | flk → | predicted flagella assembly protein |
| RA | 1,533,542 | G→A | 35.4% | P51S (CCT→TCT) | prmB ← | N5‑glutamine methyltransferase |
| RA | 1,544,443 | G→A | 9.7% | L427F (CTT→TTT) | yfcY ← | beta‑ketoacyl‑CoA thiolase, anaerobic, subunit |
| RA | 1,598,488 | C→T | 37.2% | A60A (GCG→GCA) | yfeT ← | predicted DNA‑binding transcriptional regulator |
| RA | 1,697,632 | A→G | 22.4% | Y195C (TAT→TGT) | yfhR → | predicted peptidase |
| RA | 1,747,876 | G→A | 28.6% | S44L (TCA→TTA) | yfiE ← | predicted DNA‑binding transcriptional regulator |
| RA | 1,763,556 | T→C | 33.6% | noncoding (288/1542 nt) | rrsG ← | 16S ribosomal RNA |
| RA | 1,798,695 | A→G | 37.7% | Q239R (CAA→CGA) | proV → | glycine betaine transporter subunit |
| RA | 1,807,377 | T→C | 25.2% | intergenic (+58/+6) | emrB → / ← luxS | multidrug efflux system protein/S‑ribosylhomocysteinase |
| RA | 1,827,932 | C→T | 33.8% | A392V (GCG→GTG) | mutS → | methyl‑directed mismatch repair protein |
| RA | 1,834,094 | A→G | 32.3% | D65G (GAT→GGT) | ygbM → | conserved hypothetical protein |
| RA | 1,845,199 | G→T | 58.3% | P266T (CCG→ACG) | cysD ← | sulfate adenylyltransferase, subunit 2 |
| RA | 1,874,329 | A→G | 37.7% | I191T (ATT→ACT) | ygcF ← | conserved hypothetical protein |
| RA | 1,883,198 | A→G | 26.4% | F429L (TTC→CTC) | rumA ← | 23S rRNA (uracil‑5)‑methyltransferase |
| RA | 1,890,961 | G→A | 25.8% | 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 | 27.0% | E208E (GAA→GAG) | ptsP ← | fused PEP‑protein phosphotransferase (enzyme I) of PTS system |
| RA | 1,993,572 | G→A | 35.0% | V289M (GTG→ATG) | nupG → | nucleoside transporter |
| RA | 2,004,302 | G→A | 25.5% | S483F (TCT→TTT) | hybC ← | hydrogenase 2, large subunit |
| RA | 2,144,345 | G→A | 31.0% | D206N (GAT→AAT) | argG → | argininosuccinate synthetase |
| RA | 2,211,683 | A→G | 30.1% | I465I (ATT→ATC) | rng ← | ribonuclease G |
| RA | 2,236,903 | G→A | 27.7% | A150T (GCT→ACT) | purD → | phosphoribosylglycinamide synthetase phosphoribosylamine‑glycine ligase |
| RA | 2,248,116:1 | +G | 12.0% | coding (1829/1896 nt) | thiC → | thiamin (pyrimidine moiety) biosynthesis protein |
| RA | 2,249,490 | G→A | 29.8% | S227N (AGC→AAC) | thiF → | thiamin (thiazole moiety) biosynthesis protein |
| RA | 2,266,165 | G→A | 8.5% | I93I (ATC→ATT) | tufB ← | protein chain elongation factor EF‑Tu |
| RA | 2,283,783 | G→T | 24.0% | L39M (CTG→ATG) | oxyR ← | DNA‑binding transcriptional dual regulator |
| RA | 2,321,698 | G→A | 22.8% | T93I (ACC→ATC) | cdh ← | CDP‑diacylglycerol phosphotidylhydrolase |
| RA | 2,355,216 | T→C | 5.7% | Y328C (TAT→TGT) | yihE ← | predicted kinase |
| RA | 2,355,219 | A→C | 6.1% | M327R (ATG→AGG) | yihE ← | predicted kinase |
| RA | 2,359,867 | G→A | 50.5% | noncoding (1228/2905 nt) | rrlA ← | 23S ribosomal RNA |
| RA | 2,359,876 | C→T | 40.6% | noncoding (1219/2905 nt) | rrlA ← | 23S ribosomal RNA |
| RA | 2,384,474 | G→A | 13.3% | L363L (CTG→TTG) | metE ← | 5‑methyltetrahydropteroyltriglutamate‑ homocysteine S‑methyltransferase |
| RA | 2,384,489 | G→A | 13.3% | L358L (CTG→TTG) | metE ← | 5‑methyltetrahydropteroyltriglutamate‑ homocysteine S‑methyltransferase |
| RA | 2,384,502 | G→A | 16.2% | C353C (TGC→TGT) | metE ← | 5‑methyltetrahydropteroyltriglutamate‑ homocysteine S‑methyltransferase |
| RA | 2,384,511 | T→C | 17.6% | L350L (CTA→CTG) | metE ← | 5‑methyltetrahydropteroyltriglutamate‑ homocysteine S‑methyltransferase |
| RA | 2,433,213 | T→C | 13.8% | I77I (ATT→ATC) | rhlB → | ATP‑dependent RNA helicase |
| RA | 2,433,215 | C→G | 14.0% | A78G (GCC→GGC) | rhlB → | ATP‑dependent RNA helicase |
| RA | 2,433,217 | G→A | 14.1% | D79N (GAT→AAT) | rhlB → | ATP‑dependent RNA helicase |
| RA | 2,441,897 | C→T | 26.5% | L462L (TTG→TTA) | ilvA ← | threonine deaminase |
| RA | 2,513,416 | T→C | 22.3% | F203S (TTT→TCT) | gltS → | glutamate transporter |
| RA | 2,523,040 | T→C | 31.9% | K225K (AAA→AAG) | dinD ← | DNA‑damage‑inducible protein |
| RA | 2,528,498 | C→T | 44.9% | D83N (GAT→AAT) | dfp ← | fused 4'‑phosphopantothenoylcysteine decarboxylase and phosphopantothenoylcysteine synthetase, FMN‑binding |
| RA | 2,530,398 | G→A | 23.8% | A26T (GCA→ACA) | mutM → | formamidopyrimidine/5‑formyluracil/ 5‑hydroxymethyluracil DNA glycosylase |
| RA | 2,531,609 | A→G | 24.0% | I14I (ATT→ATC) | coaD ← | pantetheine‑phosphate adenylyltransferase |
| RA | 2,540,373 | G→T | 24.9% | D300Y (GAT→TAT) | rfaJ → | UDP‑D‑glucose:(galactosyl)lipopolysaccharide glucosyltransferase |
| RA | 2,572,558 | A→G | 6.2% | intergenic (+1326/‑453) | yibH → / → ysaB | hypothetical protein/hypothetical protein |
| RA | 2,599,135 | A→T | 18.8% | I33I (ATT→ATA) | gor ← | glutathione oxidoreductase |
| RA | 2,677,626 | C→T | 27.0% | A102T (GCA→ACA) | yhgA ← | predicted transposase |
| RA | 2,687,159 | G→A | 26.2% | L374L (CTG→TTG) | pck ← | phosphoenolpyruvate carboxykinase |
| RA | 2,732,305:1 | +G | 22.9% | coding (375/723 nt) | yheO → | predicted DNA‑binding transcriptional regulator |
| RA | 2,732,642 | C→A | 25.2% | Q238K (CAA→AAA) | yheO → | predicted DNA‑binding transcriptional regulator |
| RA | 2,828,639 | C→A | 12.4% | A451S (GCG→TCG) | aspA ← | aspartate ammonia‑lyase |
| RA | 2,850,177 | G→A | 36.8% | Q286* (CAG→TAG) | yjeP ← | predicted mechanosensitive channel |
| RA | 2,858,845 | G→A | 14.1% | S373S (TCG→TCA) | amiB → | N‑acetylmuramoyl‑l‑alanine amidase II |
| RA | 2,864,584 | C→T | 14.0% | A295A (GCC→GCT) | hflK → | modulator for HflB protease specific for phage lambda cII repressor |
| RA | 2,912,429 | C→T | 35.9% | A135T (GCG→ACG) | pyrI ← | aspartate carbamoyltransferase, regulatory subunit |
| RA | 2,947,335 | A→G | 21.1% | L158P (CTG→CCG) | dnaT ← | DNA biosynthesis protein |
| RA | 2,948,123 | T→C | 21.4% | T40A (ACC→GCC) | yjjB ← | conserved inner membrane protein |
| RA | 2,971,396 | T→C | 35.9% | V71A (GTG→GCG) | serB → | 3‑phosphoserine phosphatase |
| RA | 2,986,542 | A→G | 26.9% | 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 | 444389 | 444428 | 40 | 11 [9] | [7] 11 | kdpE | DNA‑binding response regulator in two‑component regulatory system with KdpD |
| * | * | ÷ | minE | 899425 | 899447 | 23 | 10 [7] | [8] 11 | pspD | peripheral inner membrane phage‑shock protein |
| * | * | ÷ | minE | 1616724 | 1616750 | 27 | 10 [9] | [7] 13 | eutE | predicted aldehyde dehydrogenase, ethanolamine utilization protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | minE | = 1886614 | 73 (1.170) | 35 (0.680) +AAGACAAAT |
5/82 | NT | 29.1% | coding (2076/2757 nt) | barA | hybrid sensory histidine kinase, in two‑component regulatory system with UvrY |
| ? | minE | = 2149918 | 136 (2.170) | coding (87/849 nt) | folP | 7,8‑dihydropteroate synthase | |||||