mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.32.0 revision 6ff6de7d1b87
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 37,284 | T→G | 15.0% | T181P (ACC→CCC) | caiC ← | putative crotonobetaine/carnitine‑CoA ligase |
| RA | 48,555 | A→G | 18.7% | S263G (AGC→GGC) | kefC → | potassium:proton antiporter |
| RA | 71,877 | A→G | 18.0% | E176G (GAG→GGG) | yabI → | DedA family inner membrane protein |
| RA | 175,537 | T→G | 24.1% | V144G (GTG→GGG) | clcA → | H(+)/Cl(‑) exchange transporter |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 265,266 | T→G | 15.0% | intergenic (‑60/+38) | yafX ← / ← ykfF | CP4‑6 prophage, uncharacterized protein/CP4‑6 prophage, uncharacterized protein |
| RA | 361,668 | C→T | 15.1% | E65K (GAA→AAA) | lacA ← | thiogalactoside acetyltransferase |
| RA | 417,593 | A→G | 17.9% | E151G (GAG→GGG) | phoB → | response regulator in two‑component regulatory system with PhoR |
| RA | 421,608 | T→G | 25.1% | V208G (GTG→GGG) | proY → | proline‑specific permease |
| RA | 422,231 | A→T | 15.8% | I416F (ATC→TTC) | proY → | proline‑specific permease |
| RA | 429,830 | T→G | 17.7% | V109G (GTG→GGG) | secF → | SecYEG protein translocase auxillary subunit |
| RA | 550,033 | A→G | 14.3% | E136G (GAG→GGG) | ylbF → | putative anaerobic allantoin catabolic oxamate carbamoyltransferase, DUF2877 family protein |
| RA | 647,210 | A→C | 26.7% | G100G (GGT→GGG) | citG ← | 2‑(5''‑triphosphoribosyl)‑3'‑dephosphocoenzyme‑A synthase |
| RA | 742,886 | T→G | 13.7% | S20R (AGT→AGG) | ybgI → | NIF3 family metal‑binding protein |
| RA | 816,792 | C→A | 20.0% | intergenic (‑145/‑252) | ybhK ← / → moaA | putative CofD superfamily transferase/molybdopterin biosynthesis protein A |
| RA | 884,189 | A→G | 32.4% | M173V (ATG→GTG) | mdfA → | multidrug efflux system protein |
| RA | 896,963 | A→G | 14.0% | E277G (GAG→GGG) | potH → | putrescine ABC transporter permease |
| RA | 1,009,126 | A→T | 11.8% | Y428F (TAT→TTT) | rlmL → | 23S rRNA m(2)G2445 and m(7)G2069 methyltransferases, SAM‑dependent |
| RA | 1,021,591 | T→G | 15.3% | C152G (TGT→GGT) | sxy → | CRP‑S‑dependent promoter expression factor |
| RA | 1,058,486 | T→C | 19.2% | S135P (TCG→CCG) | torC → | trimethylamine N‑oxide (TMAO) reductase I, cytochrome c‑type subunit |
| RA | 1,062,576 | G→A | 9.0% | L94F (CTT→TTT) | cbpM ← | modulator of CbpA co‑chaperone |
| RA | 1,158,048 | A→C | 24.6% | P60P (CCA→CCC) | ptsG → | fused glucose‑specific PTS enzymes: IIB component/IIC component |
| RA | 1,196,131 | G→A | 28.2% | A337T (GCC→ACC) | icd → | isocitrate dehydrogenase, e14 prophage attachment site, tellurite reductase |
| RA | 1,196,305 | C→T | 54.4% | R395C (CGT→TGT) | icd → | isocitrate dehydrogenase, e14 prophage attachment site, tellurite reductase |
| RA | 1,242,926 | T→C | 13.6% | E52G (GAG→GGG) | ldcA ← | murein tetrapeptide carboxypeptidase, LD‑carboxypeptidase A |
| RA | 1,286,612 | A→T | 16.4% | intergenic (+86/+454) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,335,743 | A→T | 18.2% | intergenic (+285/‑88) | yciX → / → acnA | uncharacterized protein/aconitate hydratase 1, aconitase A |
| RA | 1,400,026 | C→A | 13.4% | A71S (GCC→TCC) | ogt ← | O‑6‑alkylguanine‑DNA:cysteine‑protein methyltransferase |
| RA | 1,472,791 | A→G | 17.6% | pseudogene (2275/3497 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,722,908 | T→C | 12.7% | L263P (CTC→CCC) | ydhK → | putative efflux protein (PET) component of YdhJK efflux pump |
| RA | 1,825,164 | A→T | 14.1% | G154G (GGT→GGA) | spy ← | periplasmic ATP‑independent protein refolding chaperone, stress‑induced |
| RA | 1,825,226 | G→T | 15.2% | Q134K (CAG→AAG) | spy ← | periplasmic ATP‑independent protein refolding chaperone, stress‑induced |
| RA | 1,854,796 | A→C | 19.0% | V20G (GTG→GGG) | ydjF ← | putative DNA‑binding transcriptional regulator |
| RA | 1,874,824 | C→G | 10.5% | T251T (ACG→ACC) | yeaM ← | putative DNA‑binding transcriptional regulator |
| RA | 1,976,691 | T→C | 13.3% | E150G (GAG→GGG) | motA ← | proton conductor component of flagella motor |
| RA | 1,977,719 | T→G | 16.9% | K42N (AAA→AAC) | flhC ← | flagellar class II regulon transcriptional activator, with FlhD |
| RA | 1,991,593 | A→C | 13.7% | S9R (AGT→AGG) | yecA ← | UPF0149 family protein |
| RA | 2,041,102 | A→G | 7.6% | N207S (AAC→AGC) | yedZ → | inner membrane heme subunit for periplasmic YedYZ reductase |
| RA | 2,126,490 | T→C | 16.7% | E234G (GAG→GGG) | wcaG ← | bifunctional GDP‑fucose synthetase: GDP‑4‑dehydro‑6‑deoxy‑D‑mannose epimerase/ GDP‑4‑dehydro‑6‑L‑deoxygalactose reductase |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,260,627 | T→C | 20.9% | E261G (GAG→GGG) | fruA ← | fused fructose‑specific PTS enzymes: IIBcomponent/IIC components |
| RA | 2,303,241 | A→G | 16.7% | S85S (TCT→TCC) | napF ← | ferredoxin‑type protein, role in electron transfer to periplasmic nitrate reductase NapA |
| RA | 2,308,456 | T→C | 11.8% | E53G (GAG→GGG) | yojI ← | microcin J25 efflux ABC transporter permease/ATPase |
| RA | 2,355,456 | T→G | 13.5% | G398G (GGT→GGG) | glpB → | anaerobic sn‑glycerol‑3‑phosphate dehydrogenase membrane anchor subunit |
| RA | 2,410,688:1 | +G | 6.3% | coding (663/1833 nt) | yfbS ← | putative transporter |
| RA | 2,504,650 | A→C | 28.0% | V299G (GTG→GGG) | ypdE ← | aminopeptidase |
| RA | 2,748,339 | A→C | 14.1% | H127P (CAC→CCC) | ypjD → | cytochrome c assembly protein family inner membrane protein |
| RA | 2,791,436 | G→C | 13.0% | A56P (GCC→CCC) | gabD → | succinate‑semialdehyde dehydrogenase I, NADP‑dependent |
| RA | 2,791,796 | A→C | 20.3% | T176P (ACC→CCC) | gabD → | succinate‑semialdehyde dehydrogenase I, NADP‑dependent |
| RA | 2,812,243 | T→C | 4.8% | T273T (ACT→ACC) | emrA → | multidrug efflux system |
| RA | 2,909,227 | A→C | 15.9% | G146G (GGT→GGG) | pyrG ← | CTP synthetase |
| RA | 2,936,841 | T→C | 15.2% | S420S (TCT→TCC) | fucI → | L‑fucose isomerase |
| RA | 2,975,091 | T→G | 18.4% | T308P (ACT→CCT) | aas ← | fused 2‑acylglycerophospho‑ethanolamine acyl transferase/acyl‑acyl carrier protein synthetase |
| RA | 2,978,164 | T→A | 28.6% | Y245F (TAT→TTT) | lysA ← | diaminopimelate decarboxylase, PLP‑binding |
| RA | 2,984,494 | A→C | 13.6% | V366G (GTG→GGG) | yqeF ← | short chain acyltransferase |
| JC | 3,007,864:1 | (ACC)3→4 | 8.7% | coding (357/1197 nt) | ygeX → | 2,3‑diaminopropionate ammonia lyase, PLP‑dependent |
| RA | 3,022,272 | T→G | 16.3% | V320G (GTG→GGG) | xdhD → | putative hypoxanthine oxidase, molybdopterin‑binding/Fe‑S binding |
| RA | 3,051,837 | A→C | 13.2% | V160G (GTG→GGG) | ubiI ← | 2‑octaprenylphenol hydroxylase, FAD‑dependent |
| RA | 3,053,583 | T→G | 26.6% | N419T (AAC→ACC) | pepP ← | proline aminopeptidase P II |
| RA | 3,070,793 | A→G | 11.1% | S150S (TCT→TCC) | fbaA ← | fructose‑bisphosphate aldolase, class II |
| RA | 3,206,436 | G→A | 24.6% | intergenic (‑182/‑25) | ttdR ← / → ttdA | transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,475 | T→A | 27.4% | S5R (AGT→AGA) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,504 | C→A | 24.1% | T15K (ACA→AAA) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,216,973 | T→G | 18.0% | V66G (GTG→GGG) | yqjI → | PadR family putative transcriptional regulator |
| RA | 3,239,394 | C→T | 13.8% | L273L (CTG→TTG) | alx → | putative membrane‑bound redox modulator |
| RA | 3,255,499 | G→C | 25.6% | A384G (GCG→GGG) | yhaM ← | putative L‑serine dehydratase alpha chain |
| RA | 3,277,507 | A→G | 13.0% | E58G (GAG→GGG) | yhaV → | toxin of the SohB(PrlF)‑YhaV toxin‑antitoxin system |
| RA | 3,287,637 | A→C | 18.2% | T72P (ACT→CCT) | yraH → | putative fimbrial‑like adhesin protein |
| RA | 3,289,076 | C→A | 14.8% | Q89K (CAG→AAG) | yraJ → | putative outer membrane protein |
| RA | 3,293,685 | T→C | 17.6% | A96A (GCT→GCC) | lpoA → | OM lipoprotein stimulator of MrcA transpeptidase |
| RA | 3,300,862 | T→C | 15.6% | E138G (GAG→GGG) | yhbT ← | SCP‑2 sterol transfer family protein |
| RA | 3,376,874 | T→C | 8.2% | E182G (GAG→GGG) | sspA ← | stringent starvation protein A, phage P1 late gene activator, RNAP‑associated acid‑resistance protein, inactive glutathione S‑transferase homolog |
| RA | 3,403,735 | T→C | 7.3% | L85P (CTC→CCC) | acuI → | putative acryloyl‑CoA reductase |
| RA | 3,414,308 | T→C | 18.0% | A149A (GCT→GCC) | acrE → | cytoplasmic membrane lipoprotein |
| RA | 3,416,440 | C→T | 13.7% | F470F (TTC→TTT) | acrF → | multidrug efflux system protein |
| RA | 3,421,767 | G→T | 20.6% | E149* (GAG→TAG) | yhdY → | putative amino acid ABC transporter permease |
| RA | 3,479,687 | G→A | 22.4% | L307F (CTC→TTC) | kefB ← | potassium:proton antiporter |
| RA | 3,489,860 | A→G | 21.9% | S107P (TCC→CCC) | argD ← | bifunctional acetylornithine aminotransferase and succinyldiaminopimelate aminotransferase |
| RA | 3,536,121 | G→C | 19.7% | R154R (CGC→CGG) | ompR ← | response regulator in two‑component regulatory system with EnvZ |
| RA | 3,560,493 | G→A | 16.2% | pseudogene (111/149 nt) | glpR ← | pseudogene, DNA‑binding transcriptional repressor,regulator, Energy metabolism, carbon: Anaerobic respiration, repressor of the glp operon |
| RA | 3,686,538 | T→C | 13.0% | S879G (AGC→GGC) | bcsC ← | cellulose synthase subunit |
| RA | 3,689,746 | T→C | 16.4% | E172G (GAG→GGG) | bcsZ ← | endo‑1,4‑D‑glucanase |
| RA | 3,748,910 | A→G | 12.3% | E112G (GAG→GGG) | sgbH → | 3‑keto‑L‑gulonate 6‑phosphate decarboxylase |
| RA | 3,749,428 | T→G | 18.8% | G66G (GGT→GGG) | sgbU → | putative L‑xylulose 5‑phosphate 3‑epimerase |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,824,731 | T→G | 22.1% | V73G (GTG→GGG) | trmH → | tRNA mG18‑2'‑O‑methyltransferase, SAM‑dependent |
| RA | 3,842,178 | A→C | 6.9% | V75G (GTG→GGG) | yicN ← | DUF1198 family protein |
| RA | 3,862,676 | G→C | 32.7% | pseudogene (927/1617 nt) | glvC ← | pseudogene, arbutin specific enzyme IIC component of PTS,enzyme, Transport of small molecules: Carbohydrates, organic acids, alcohols, PTS system, arbutin‑like IIB component, PTS system, arbutin‑like IIC component |
| RA | 3,916,431 | T→G | 11.3% | H315P (CAC→CCC) | atpD ← | F1 sector of membrane‑bound ATP synthase, beta subunit |
| RA | 3,931,522 | A→C | 12.3% | T70P (ACC→CCC) | kup → | potassium transporter |
| RA | 3,949,064 | T→C | 12.2% | E302G (GAG→GGG) | yifB ← | magnesium chelatase family protein and putative transcriptional regulator |
| RA | 4,001,388 | G→A | 5.0% | intergenic (‑333/‑37) | yigE ← / → corA | DUF2233 family protein/magnesium/nickel/cobalt transporter |
| JC | 4,001,644 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,017,124 | A→G | 8.8% | E232G (GAG→GGG) | udp → | uridine phosphorylase |
| RA | 4,057,715 | A→G | 7.9% | S107P (TCC→CCC) | glnA ← | glutamine synthetase |
| RA | 4,062,917 | C→T | 3.3% | I224I (ATC→ATT) | yihN → | MFS transporter family protein |
| RA | 4,142,645 | G→T | 19.8% | L39F (TTG→TTT) | frwC → | putative enzyme IIC component of PTS |
| RA | 4,158,652 | T→G | 12.1% | V55G (GTG→GGG) | oxyR → | oxidative and nitrosative stress transcriptional regulator |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,219,538 | C→T | 10.6% | A315V (GCG→GTG) | aceK → | isocitrate dehydrogenase kinase/phosphatase |
| RA | 4,228,796 | T→G | 13.7% | V356G (GTG→GGG) | yjbB → | putative Na+/Pi‑cotransporter |
| RA | 4,285,483 | A→G | 11.7% | S630P (TCG→CCG) | acs ← | acetyl‑CoA synthetase |
| RA | 4,295,699 | T→G | 20.1% | V407G (GTG→GGG) | gltP → | glutamate/aspartate:proton symporter |
| RA | 4,359,250 | A→C | 15.8% | S261R (AGT→AGG) | cadB ← | putative lysine/cadaverine transporter |
| RA | 4,368,956 | C→T | 20.0% | L98L (CTA→TTA) | fxsA → | suppressor of F exclusion of phage T7 |
| RA | 4,430,346 | A→G | 14.7% | E161G (GAG→GGG) | cycA → | D‑alanine/D‑serine/glycine transporter |
| RA | 4,442,011 | A→C | 17.0% | V56G (GTG→GGG) | msrA ← | methionine sulfoxide reductase A |
| RA | 4,480,112 | C→T | 11.4% | L128F (CTC→TTC) | yjgN → | DUF898 family inner membrane protein |
| RA | 4,502,757 | C→T | 18.5% | E226K (GAA→AAA) | insG ← | IS4 transposase |
| RA | 4,587,590 | A→G | 14.8% | E214G (GAG→GGG) | mrr → | methylated adenine and cytosine restriction protein |
| RA | 4,606,903 | A→G | 25.2% | S267P (TCC→CCC) | rsmC ← | 16S rRNA m(2)G1207 methyltransferase, SAM‑dependent |
| RA | 4,614,396 | T→C | 7.7% | intergenic (+135/+285) | yjjV → / ← yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
| RA | 4,614,403 | C→T | 7.8% | intergenic (+142/+278) | yjjV → / ← yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 2470092 | 2470451 | 360 | 21 [16] | [16] 20 | gtrS | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| * | * | ÷ | NC_000913 | 4233765 | 4235437 | 1673 | 19 [18] | [16] 20 | [pgi] | [pgi] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 166895 = | 96 (1.260) | 3 (0.040) | 3/412 | NT | 3.1% | coding (2166/2535 nt) | mrcB | fused glycosyl transferase and transpeptidase |
| ? | NC_000913 | 166923 = | 93 (1.260) | coding (2194/2535 nt) | mrcB | fused glycosyl transferase and transpeptidase | |||||
| * | ? | NC_000913 | 257908 = | NA (NA) | 77 (1.010) | 57/426 | NT | 98.7% | intergenic (+9/‑768) | crl/crl | pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers/pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers |
| ? | NC_000913 | = 1293039 | 1 (0.010) | intergenic (‑117/‑488) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase | |||||
| * | ? | NC_000913 | 458787 = | 50 (0.660) | 28 (0.370) | 24/420 | NT | 36.2% | intergenic (+87/‑101) | clpX/lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| ? | NC_000913 | 608011 = | NA (NA) | intergenic (+23/‑54) | hokE/insL1 | toxic polypeptide, small/IS186 transposase | |||||
| * | ? | NC_000913 | = 458799 | 48 (0.630) | 35 (0.470) | 31/418 | NT | 42.6% | intergenic (+99/‑89) | clpX/lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| ? | NC_000913 | = 609347 | NA (NA) | intergenic (+170/+112) | insL1/entD | IS186 transposase/phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex | |||||
| * | ? | NC_000913 | 1207790 = | 22 (0.290) | 74 (1.050) | 53/394 | NT | 86.4% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 3 (0.040) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 23 (0.300) | 83 (1.180) | 54/394 | NT | 87.2% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 3 (0.040) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 0 (0.000) | 83 (1.090) | 52/426 | NT | 100% | intergenic (‑110/‑495) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| ? | NC_000913 | = 1979270 | NA (NA) | intergenic (‑55/‑483) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 29 (0.390) | 25/418 | 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 | = 1978502 | 0 (0.000) | 41 (0.560) | 33/410 | NT | 100% | intergenic (‑305/+16) | flhD/insB1 | flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B |
| ? | NC_000913 | 1979279 = | 0 (0.000) | intergenic (‑64/‑474) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | 1979486 = | 0 (0.000) | 34 (0.450) | 27/426 | NT | 100% | intergenic (‑271/‑267) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | 2101749 = | NA (NA) | intergenic (‑5/+146) | wbbL/insH1 | pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator | |||||
| * | ? | NC_000913 | = 1979489 | 0 (0.000) | 77 (1.010) | 53/426 | NT | 100% | intergenic (‑274/‑264) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | = 2290111 | NA (NA) | intergenic (‑32/+1) | insH1/yejO | IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system | |||||
| * | ? | NC_000913 | = 2852111 | 51 (0.670) | 4 (0.050) | 4/410 | NT | 7.3% | coding (250/273 nt) | hypC | hydrogenase maturation protein |
| ? | NC_000913 | = 2852155 | 53 (0.720) | coding (22/1122 nt) | hypD | hydrogenase maturation protein | |||||