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 | 32,807 | C→A | 6.0% | T664N (ACC→AAC) | carB → | carbamoyl‑phosphate synthase large subunit |
| RA | 114,203 | C→T | 6.0% | R254C (CGC→TGC) | guaC → | GMP reductase |
| RA | 129,076 | G→A | 5.0% | A389T (GCT→ACT) | lpd → | dihydrolipoyl dehydrogenase; E3 component of pyruvate and 2‑oxoglutarate dehydrogenases complexes; glycine cleavage system L protein; dihydrolipoamide dehydrogenase |
| JC JC | 168,640 | IS2 (+) +5 bp | 100% | coding (1157‑1161/2244 nt) | fhuA → | ferrichrome outer membrane transporter |
| RA | 191,997 | G→A | 5.6% | G48D (GGT→GAT) | pyrH → | uridylate kinase |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 342,393 | C→T | 8.2% | D423D (GAC→GAT) | yahJ → | putative metallo‑dependent hydrolase domain deaminase |
| RA | 386,011 | A→T | 5.8% | E260D (GAA→GAT) | tauA → | taurine ABC transporter periplasmic binding protein |
| RA | 405,463 | G→A | 5.3% | A61V (GCG→GTG) | proC ← | pyrroline‑5‑carboxylate reductase, NAD(P)‑binding |
| RA | 414,144 | T→G | 6.2% | N537T (AAC→ACC) | sbcC ← | exonuclease, dsDNA, ATP‑dependent |
| RA | 422,062 | G→A | 5.4% | V359V (GTG→GTA) | proY → | proline‑specific permease |
| RA | 467,238 | G→T | 5.1% | T25T (ACC→ACA) | ybaE ← | putative ABC transporter periplasmic binding protein |
| RA | 470,045 | A→T | 5.2% | D392V (GAT→GTT) | mdlA → | putative multidrug ABC transporter ATPase |
| RA | 470,515 | G→A | 5.0% | A549T (GCC→ACC) | mdlA → | putative multidrug ABC transporter ATPase |
| RA | 473,997 | C→T | 8.5% | G344G (GGC→GGT) | amtB → | ammonium transporter |
| RA | 555,233 | A→T | 6.3% | E208V (GAA→GTA) | cysS → | cysteinyl‑tRNA synthetase |
| RA | 596,222 | G→T | 7.1% | S208I (AGC→ATC) | cusC → | copper/silver efflux system, outer membrane component |
| RA | 627,738 | C→T | 6.9% | H15H (CAC→CAT) | entB → | isochorismatase |
| RA | 698,393 | T→C | 5.8% | E262G (GAA→GGA) | asnB ← | asparagine synthetase B |
| RA | 716,326 | C→T | 8.0% | pseudogene (272/651 nt) | ybfG ← | pseudogene |
| RA | 787,359 | C→T | 6.1% | L79L (CTG→CTA) | gpmA ← | phosphoglyceromutase 1 |
| RA | 829,686 | G→A | 10.2% | A96V (GCG→GTG) | ybhG ← | putative membrane fusion protein (MFP) component of efflux pump, membrane anchor |
| RA | 909,353 | G→A | 100% | A566V (GCG→GTG) | poxB ← | pyruvate dehydrogenase, thiamine triphosphate‑binding, FAD‑binding |
| JC JC | 911,086 | IS2 (–) +5 bp | 100% | intergenic (‑37/+92) | poxB ← / ← hcr | pyruvate dehydrogenase, thiamine triphosphate‑binding, FAD‑binding/HCP oxidoreductase, NADH‑dependent |
| RA | 926,398 | T→C | 5.1% | T16A (ACG→GCG) | infA ← | translation initiation factor IF‑1 |
| RA | 951,524 | T→C | 6.3% | K677K (AAA→AAG) | pflB ← | formate C‑acetyltransferase 1, anaerobic; pyruvate formate‑lyase 1 |
| RA | 981,097 | C→A | 7.1% | C17* (TGC→TGA) | ldtD → | murein L,D‑transpeptidase |
| RA | 999,964 | T→C | 5.2% | V250A (GTA→GCA) | elfC → | putative outer membrane fimbrial subunit export usher protein |
| RA | 1,014,199 | C→T | 5.8% | T314I (ACC→ATC) | pqiB → | paraquat‑inducible, SoxRS‑regulated MCE domain protein |
| RA | 1,046,089 | G→A | 7.3% | S619S (AGC→AGT) | gfcD ← | putative O‑antigen capsule production periplasmic protein |
| RA | 1,126,716 | A→T | 5.4% | D187V (GAT→GTT) | yceH → | UPF0502 family protein |
| RA | 1,130,038 | C→T | 5.1% | A31T (GCA→ACA) | flgM ← | anti‑sigma factor for FliA (sigma 28) |
| RA | 1,158,773 | T→C | 5.9% | F302S (TTC→TCC) | ptsG → | fused glucose‑specific PTS enzymes: IIB component/IIC component |
| RA | 1,158,881 | C→T | 100% | S338L (TCG→TTG) | ptsG → | fused glucose‑specific PTS enzymes: IIB component/IIC component |
| RA | 1,161,067 | C→T | 6.3% | R162H (CGT→CAT) | fhuE ← | ferric‑rhodotorulic acid outer membrane transporter |
| RA | 1,172,148 | G→A | 7.4% | A606V (GCG→GTG) | mfd ← | transcription‑repair coupling factor |
| RA | 1,211,424 | T→C | 9.5% | pseudogene (12/165 nt) | icdC → | pseudogene, isocitrate dehydrogenase C‑terminal gene fragment; idcC' is a 54 codon 3' gene fragment created during e14 prophage insertion |
| RA | 1,258,185 | C→T | 6.0% | G110D (GGC→GAC) | pth ← | peptidyl‑tRNA hydrolase |
| RA | 1,286,067 | G→A | 8.7% | P73P (CCG→CCA) | narI → | nitrate reductase 1, gamma (cytochrome b(NR)) subunit |
| 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 |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,301,823 | C→T | 5.2% | N214N (AAC→AAT) | oppA → | oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,303,990 | G→A | 9.9% | V53I (GTA→ATA) | oppC → | oligopeptide ABC transporter permease |
| RA | 1,426,842 | A→G | 5.1% | pseudogene (389/933 nt) | tmpR → | Rac prophage; pseudogene, tail protein family;Phage or Prophage Related; putative alpha helix protein |
| RA | 1,437,993 | G→A | 5.2% | A931V (GCT→GTT) | pfo ← | pyruvate‑flavodoxin oxidoreductase |
| RA | 1,569,308 | A→G | 6.3% | L394L (CTT→CTC) | gadC ← | glutamate:gamma‑aminobutyric acid antiporter |
| RA | 1,575,620 | G→A | 5.9% | A667V (GCA→GTA) | yddB ← | putative TonB‑dependent outer membrane receptor |
| RA | 1,760,433 | C→T | 5.2% | A31T (GCC→ACC) | sufS ← | cysteine desulfurase, stimulated by SufE; selenocysteine lyase, PLP‑dependent |
| RA | 1,830,829 | T→C | 8.3% | E385G (GAG→GGG) | astC ← | succinylornithine transaminase, PLP‑dependent |
| RA | 1,841,764 | C→T | 8.6% | T92M (ACG→ATG) | nudG → | CTP pyrophosphohydrolase; also hydrolyzes 2‑hydroxy‑dATP, 8‑hydroxy‑dGTP, 5‑hydroxy‑CTP, dCTP and 5‑methyl‑dCTP |
| RA | 1,872,748 | G→A | 5.8% | V236V (GTG→GTA) | yeaJ → | putative diguanylate cyclase |
| RA | 1,890,091 | G→C | 6.9% | H148D (CAT→GAT) | yeaY ← | Slp family lipoprotein, RpoE‑regulated |
| RA | 1,899,169 | C→T | 6.2% | A248V (GCG→GTG) | yoaD → | putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase, regulator of cellulose production |
| RA | 1,904,339 | C→T | 6.0% | L149L (CTG→TTG) | manZ → | mannose‑specific enzyme IID component of PTS |
| RA | 1,916,484 | T→A | 7.4% | M76K (ATG→AAG) | yebS → | inner membrane PqiA domain protein |
| RA | 1,927,030 | G→T | 5.1% | Q604K (CAG→AAG) | ptrB ← | protease II |
| RA | 1,947,359 | G→A | 8.7% | G6G (GGC→GGT) | ruvC ← | component of RuvABC resolvasome, endonuclease |
| RA | 1,973,263 | T→C | 8.7% | D26G (GAT→GGT) | cheW ← | purine‑binding chemotaxis protein |
| 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 | 2,021,984 | Δ1 bp | 6.0% | coding (116/738 nt) | fliP → | flagellar biosynthesis protein |
| RA | 2,075,061 | T→C | 5.9% | S95P (TCT→CCT) | yeeR → | CP4‑44 prophage; putative membrane protein |
| RA | 2,085,179 | T→C | 6.8% | Y116C (TAT→TGT) | yeeE ← | UPF0394 family inner membrane protein |
| RA | 2,086,469 | C→T | 6.0% | A198A (GCG→GCA) | plaP ← | putrescine importer, low affinity |
| RA | 2,120,760 | C→T | 6.0% | P265P (CCG→CCA) | wcaJ ← | colanic biosynthesis UDP‑glucose lipid carrier transferase |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| 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 |
| JC JC | 2,175,712 | IS1 (–) +9 bp | 100% | coding (602‑610/1263 nt) | gatZ ← | D‑tagatose 1,6‑bisphosphate aldolase 2, subunit |
| RA | 2,330,385 | C→T | 8.1% | pseudogene (4018/4605 nt) | yfaS ← | pseudogene, bacterial alpha2‑macroglobulin YfaS variant family; putative membrane protein |
| RA | 2,353,768 | C→T | 10.8% | G374G (GGC→GGT) | glpA → | anaerobic sn‑glycerol‑3‑phosphate dehydrogenase, large FAD/NAD(P)‑binding subunit |
| RA | 2,391,376 | C→T | 5.2% | G44R (GGG→AGG) | nuoN ← | NADH:ubiquinone oxidoreductase, membrane subunit N |
| RA | 2,413,461 | G→A | 100% | intergenic (‑329/‑9) | yfbV ← / → ackA | UPF0208 family inner membrane protein/acetate kinase A and propionate kinase 2 |
| RA | 2,469,009 | G→T | 100% | V266F (GTT→TTT) | gtrB → | CPS‑53 (KpLE1) prophage; bactoprenol glucosyl transferase |
| RA | 2,538,798 | T→C | 8.0% | G262G (GGA→GGG) | cysM ← | cysteine synthase B (O‑acetylserine sulfhydrolase B) |
| RA | 2,551,174 | G→C | 7.1% | L15V (CTG→GTG) | yfeY ← | RpoE‑regulated lipoprotein |
| RA | 2,583,110 | G→A | 7.3% | G123G (GGC→GGT) | nudK ← | GDP‑mannose pyrophosphatase |
| RA | 2,584,549 | A→G | 5.6% | V326A (GTG→GCG) | aegA ← | putative oxidoreductase, FeS binding subunit/NAD/FAD‑binding subunit |
| RA | 2,605,247 | G→A | 5.8% | G146D (GGC→GAC) | hyfD → | hydrogenase 4, membrane subunit |
| RA | 2,614,970 | C→T | 5.9% | A304A (GCG→GCA) | yfgO ← | putative UPF0118 family inner membrane permease |
| RA | 2,659,608 | C→T | 5.9% | P93P (CCG→CCA) | iscA ← | FeS cluster assembly protein |
| JC | 2,722,123 | Δ7 bp | 100% | coding (2171‑2177/2661 nt) | pka → | protein lysine acetyltransferase |
| RA | 2,829,372 | T→C | 6.9% | L109P (CTG→CCG) | srlR → | sorbitol‑inducible srl operon transcriptional repressor |
| RA | 2,834,784 | C→T | 5.6% | S291S (AGC→AGT) | norW → | NADH:flavorubredoxin oxidoreductase |
| RA | 2,933,574 | G→A | 8.9% | L39L (CTG→TTG) | fucA ← | L‑fuculose‑1‑phosphate aldolase |
| RA | 2,934,979 | G→A | 5.3% | A249T (GCA→ACA) | fucP → | L‑fucose transporter |
| RA | 3,035,437 | T→C | 82.6% | K282R (AAG→AGG) | prfB ← | peptide chain release factor RF‑2 |
| RA | 3,081,526 | G→A | 6.3% | A37V (GCC→GTC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,134,891 | A→T | 8.2% | I494K (ATA→AAA) | pitB ← | phosphate transporter |
| RA | 3,211,722 | T→C | 6.1% | F206L (TTC→CTC) | dnaG → | DNA primase |
| RA | 3,259,683 | G→A | 5.7% | intergenic (‑34/+38) | tdcG ← / ← tdcF | L‑serine dehydratase 3, anaerobic/putative reactive intermediate deaminase |
| RA | 3,302,151 | G→A | 6.9% | G223S (GGC→AGC) | yhbU → | U32 peptidase family protein |
| RA | 3,479,755 | C→T | 10.2% | G285R (GGG→AGG) | kefB ← | potassium:proton antiporter |
| RA | 3,484,760 | A→G | 6.0% | K91E (AAA→GAA) | prkB → | putative phosphoribulokinase |
| RA | 3,509,494 | A→G | 5.1% | V107A (GTG→GCG) | yhfW ← | phosphopentomutase‑related metalloenzyme superfamily 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 | 3,562,212 | C→T | 8.8% | A67V (GCG→GTG) | glpD → | sn‑glycerol‑3‑phosphate dehydrogenase, aerobic, FAD/NAD(P)‑binding |
| RA | 3,594,232 | T→C | 5.9% | N417D (AAC→GAC) | livM ← | branched‑chain amino acid ABC transporter permease |
| RA | 3,629,291 | C→T | 5.1% | R83H (CGC→CAC) | rbbA ← | ribosome‑associated ATPase: ATP‑binding protein/ATP‑binding membrane protein |
| RA | 3,699,528 | G→A | 5.1% | V439M (GTG→ATG) | bcsG → | DUF3260 family cellulose production inner membrane protein |
| JC JC | 3,771,709 | IS3 (–) +3 bp | 100% | coding (34‑36/363 nt) | yibI ← | DUF3302 family inner membrane protein |
| RA | 3,775,311 | G→T | 5.1% | Q296H (CAG→CAT) | mtlD → | mannitol‑1‑phosphate dehydrogenase, NAD‑dependent |
| RA | 3,798,652 | Δ1 bp | 100% | coding (661/1074 nt) | waaU ← | lipopolysaccharide core biosynthesis |
| RA | 3,808,813 | C→T | 6.2% | R92C (CGC→TGC) | waaA → | 3‑deoxy‑D‑manno‑octulosonic‑acid transferase (KDO transferase) |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,816,244 | T→C | 7.8% | pseudogene (306/669 nt) | rph ← | ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
| RA | 3,834,765 | C→A | 6.1% | G389* (GGA→TGA) | yicJ ← | putative transporter |
| RA | 3,850,593 | C→T | 6.2% | G45E (GGG→GAG) | uhpA ← | response regulator in two‑component regulatory system wtih UhpB |
| RA | 3,926,829 | C→T | 5.3% | V59I (GTC→ATC) | asnC ← | transcriptional activator of asnA; autorepressor |
| RA | 3,936,634 | A→T | 7.9% | K119N (AAA→AAT) | rbsB → | D‑ribose ABC transporter periplasmic binding protein; ribose chemotaxis receptor |
| RA | 3,950,784 | A→G | 5.2% | pseudogene (225/984 nt) | ilvG → | pseudogene, acetolactate synthase 2 large subunit, valine‑insensitive; acetolactate synthase II, large subunit, cryptic, interrupted |
| RA | 3,956,462 | T→A | 5.1% | C378S (TGC→AGC) | ilvA → | l‑threonine dehydratase, biosynthetic; also known as threonine deaminase |
| JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,011,492 | T→A | 6.0% | T139T (ACT→ACA) | yigM → | putative inner membrane EamA‑like transporter |
| RA | 4,021,557 | T→C | 6.5% | P444P (CCT→CCC) | ubiB → | regulator of octaprenylphenol hydroxylation, ubiquinone synthesis; regulator of 2'‑N‑acetyltransferase; putative ABC1 family protein kinase |
| RA | 4,030,251 | C→T | 5.4% | A241T (GCA→ACA) | fadB ← | fused 3‑hydroxybutyryl‑CoA epimerase/delta(3)‑cis‑delta(2)‑trans‑enoyl‑CoA isomerase/enoyl‑CoA hydratase/3‑hydroxyacyl‑CoA dehydrogenase |
| RA | 4,130,849 | C→A | 6.5% | Q339K (CAA→AAA) | metL → | Bifunctional aspartokinase/homoserine dehydrogenase 2 |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,236,466 | G→T | 5.6% | A69S (GCT→TCT) | yjbF → | extracellular polysaccharide production lipoprotein |
| RA | 4,296,060 | C→T | 20.4% | 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 | 4,320,735 | G→A | 5.1% | G171G (GGC→GGT) | phnH ← | ribophosphonate triphosphate synthase subunit |
| RA | 4,325,804 | C→T | 7.3% | intergenic (‑63/+595) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,422,372 | G→A | 5.8% | A63T (GCC→ACC) | ulaD → | 3‑keto‑L‑gulonate 6‑phosphate decarboxylase |
| RA | 4,439,556 | G→A | 6.0% | intergenic (‑294/‑31) | ytfJ ← / → ytfK | putative transcriptional regulator/DUF1107 family protein |
| RA | 4,473,613 | G→A | 6.8% | A147A (GCC→GCT) | bdcA ← | c‑di‑GMP‑binding biofilm dispersal mediator protein |
| RA | 4,509,643 | A→G | 6.2% | pseudogene (165/315 nt) | insO → | pseudogene, IS911 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,532,778 | T→A | 5.4% | M136L (ATG→TTG) | yjhP ← | putative methyltransferase |
| RA | 4,548,579 | A→G | 7.0% | K99E (AAA→GAA) | fimG → | minor component of type 1 fimbriae |
| RA | 4,626,708 | A→G | 6.3% | E266G (GAG→GGG) | radA → | DNA repair protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 123061 | 127538 | 4478 | 30 [8] | [18] 20 | [aceE]–[aceF] | [aceE],[aceF] |
| * | * | ÷ | NC_000913 | 2066303–2066464 | 2066597–2066466 | 3–295 | 19 [17] | [17] 20 | [insH1] | [insH1] |
| * | * | ÷ | NC_000913 | 3423748–3424233 | 3424549–3424238 | 6–802 | 19 [18] | [18] 20 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 26 (0.320) | 69 (0.970) | 47/216 | NT | 73.2% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 28 (0.400) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 25 (0.310) | 57 (0.810) | 42/216 | NT | 69.6% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 28 (0.400) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1411899 = | 125 (1.540) | 19 (0.300) | 18/196 | NT | 13.6% | coding (50/936 nt) | ttcA | tRNA s(2)C32 thioltransferase, iron sulfur cluster protein |
| ? | NC_000913 | = 1434958 | 142 (2.210) | pseudogene (51/51 nt) | ttcC | pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 4542682 = | 14 (0.170) | 195 (2.590) | 83/230 | NT | 94.2% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | 4542996 = | 11 (0.150) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | = 4542690 | 13 (0.160) | 202 (2.680) | 97/230 | NT | 94.6% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | = 4542986 | 11 (0.150) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||