mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 13,957 | A→T | M599L (ATG→TTG) | dnaK → | chaperone Hsp70, with co‑chaperone DnaJ |
| RA | 28,175 | T→A | W295R (TGG→AGG) | rihC → | ribonucleoside hydrolase 3 |
| RA | 101,342 | C→T | T193I (ACC→ATC) | murC → | UDP‑N‑acetylmuramate:L‑alanine ligase |
| RA | 145,691 | C→T | A204V (GCC→GTC) | yadE → | putative polysaccharide deacetylase lipoprotein |
| RA | 171,072 | A→G | K166K (AAA→AAG) | fhuD → | iron(3+)‑hydroxamate import ABC transporter periplasmic binding protein |
| RA | 243,264 | C→T | G14S (GGC→AGC) | fadE ← | acyl coenzyme A dehydrogenase |
| RA | 255,855 | A→T | intergenic (‑139/‑122) | pepD ← / → gpt | aminoacyl‑histidine dipeptidase (peptidase D)/xanthine phosphoribosyltransferase; xanthine‑guanine phosphoribosyltransferase |
| RA | 275,534 | G→A | S70S (TCG→TCA) | mmuP → | CP4‑6 prophage; putative S‑methylmethionine transporter |
| RA | 367,852 | (GC)6→5 | coding (568‑569/834 nt) | mhpR ← | mhp operon transcriptional activator |
| RA | 380,021 | (G)10→8 | intergenic (‑140/+47) | frmR ← / ← yaiO | regulator protein that represses frmRAB operon/outer membrane protein |
| RA | 432,179 | C→T | intergenic (‑166/+133) | tsx ← / ← yajI | nucleoside channel, receptor of phage T6 and colicin K/putative lipoprotein |
| RA | 484,337 | (C)6→7 | coding (67/3150 nt) | acrB ← | multidrug efflux system protein |
| RA | 619,892 | G→A | A103V (GCG→GTG) | fepC ← | ferrienterobactin ABC transporter ATPase |
| RA | 638,455 | (G)5→6 | coding (119/747 nt) | dsbG ← | thiol:disulfide interchange protein, periplasmic |
| RA | 681,304 | T→C | W365R (TGG→CGG) | djlC → | J domain‑containing HscC co‑chaperone; Hsc56 |
| RA | 714,588 | C→T | A344V (GCC→GTC) | pgm → | phosphoglucomutase |
| RA | 723,678 | A→G | V246A (GTG→GCG) | kdpD ← | fused sensory histidine kinase in two‑component regulatory system with KdpE: signal sensing protein |
| RA | 756,515 | C→T | G203G (GGC→GGT) | sdhA → | succinate dehydrogenase, flavoprotein subunit |
| RA | 826,009 | C→G | V34L (GTG→CTG) | ybhR ← | putative ABC transporter permease |
| RA | 899,184 | G→A | A223T (GCC→ACC) | rlmC → | 23S rRNA m(5)U747 methyltransferase, SAM‑dependent |
| RA | 999,709 | (C)6→7 | coding (494/2601 nt) | elfC → | putative outer membrane fimbrial subunit export usher protein |
| RA | 1,078,157 | C→T | P242P (CCG→CCA) | putA ← | fused DNA‑binding transcriptional regulator/proline dehydrogenase/pyrroline‑5‑carboxylate dehydrogenase |
| RA | 1,108,247 | A→G | I232T (ATT→ACT) | opgC ← | OPG biosynthetic transmembrane succinyltransferase |
| JC JC | 1,293,036 | IS2 (+) +5 bp | intergenic (‑114/‑487) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| RA | 1,713,019 | T→C | V84A (GTA→GCA) | dtpA → | dipeptide and tripeptide permease A |
| RA | 1,874,193 | (C)5→6 | intergenic (‑11/‑159) | yoaI ← / → yeaL | uncharacterized protein/UPF0756 family putative inner membrane protein |
| RA | 1,892,935 | +T | coding (301/1911 nt) | yoaA ← | putative ATP‑dependent helicase, DinG family |
| RA | 1,900,732 | T→C | E285G (GAA→GGA) | yoaE ← | putative membrane protein/conserved protein |
| RA | 1,968,770 | G→A | R199C (CGT→TGT) | cheR ← | chemotaxis regulator, protein‑glutamate methyltransferase |
| JC JC | 1,979,486 | IS5 (+) +4 bp | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| RA | 2,000,985 | A→G | Y14H (TAT→CAT) | fliZ ← | RpoS antagonist; putative regulator of FliA activity |
| RA | 2,054,723 | Δ1 bp | coding (1081/1317 nt) | shiA → | shikimate transporter |
| RA | 2,090,136 | (G)5→6 | intergenic (+90/‑56) | hisL → / → hisG | his operon leader peptide/ATP phosphoribosyltransferase |
| RA | 2,173,363 | Δ2 bp | intergenic (‑1/+1) | gatC ← / ← gatC | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,188,298 | T→C | A39A (GCA→GCG) | yehA ← | putative fimbrial‑like adhesin protein |
| RA | 2,245,958 | C→T | R271H (CGC→CAC) | cirA ← | colicin IA outer membrane receptor and translocator; ferric iron‑catecholate transporter |
| RA | 2,264,149 | G→A | C96Y (TGC→TAC) | setB → | lactose/glucose efflux system |
| RA | 2,267,405 | A→G | I387M (ATA→ATG) | yeiQ → | putative NAD‑dependent D‑mannonate oxidoreductase |
| RA | 2,304,838 | A→G | intergenic (+445/+270) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,314,509 | T→C | V341A (GTC→GCC) | rcsD → | phosphotransfer intermediate protein in two‑component regulatory system with RcsBC |
| RA | 2,346,140 | T→C | F426L (TTT→CTT) | nrdA → | ribonucleoside‑diphosphate reductase 1, alpha subunit |
| RA | 2,440,106 | G→A | S5S (AGC→AGT) | yfcJ ← | putative arabinose efflux transporter |
| RA | 2,446,835 | G→A | G213G (GGC→GGT) | aroC ← | chorismate synthase |
| RA | 2,566,416 | T→C | T157A (ACC→GCC) | eutA ← | reactivating factor for ethanolamine ammonia lyase |
| RA | 2,650,949 | G→A | H447Y (CAC→TAC) | yfhM ← | bacterial alpha2‑macroglobulin colonization factor ECAM; anti‑host protease defense factor; periplasmic inner membrane‑anchored lipoprotein |
| RA | 2,669,936 | G→A | R302H (CGC→CAC) | hcaE → | 3‑phenylpropionate dioxygenase, large (alpha) subunit |
| RA | 2,809,774 | (T)7→6 | coding (158/738 nt) | ygaZ → | putative L‑valine exporter, norvaline resistance protein |
| RA | 2,999,680 | (G)7→8 | coding (212/756 nt) | ygeR ← | LysM domain‑containing M23 family putative peptidase; septation lipoprotein |
| RA | 3,035,546 | T→C | T246A (ACG→GCG) | prfB ← | peptide chain release factor RF‑2 |
| RA | 3,101,039 | (C)7→8 | coding (585/720 nt) | yggN ← | DUF2884 family putative periplasmic protein |
| RA | 3,173,566 | G→C | R611G (CGC→GGC) | parE ← | DNA topoisomerase IV, subunit B |
| RA | 3,174,146 | C→T | V417V (GTG→GTA) | parE ← | DNA topoisomerase IV, subunit B |
| RA | 3,269,918 | G→A | intergenic (+316/+298) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,279,878 | A→G | D322G (GAC→GGC) | kbaZ → | tagatose 6‑phosphate aldolase 1, kbaZ subunit |
| RA | 3,305,259 | T→C | N187D (AAT→GAT) | mtr ← | tryptophan transporter of high affinity |
| RA | 3,361,329 | G→A | G52S (GGC→AGC) | gltF → | periplasmic protein |
| RA | 3,379,259 | T→C | K247E (AAA→GAA) | zapE ← | divisome ATPase |
| RA | 3,560,455 | +G | 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 |
| MC JC | 3,815,859 | Δ82 bp | [rph]–[rph] | [rph], [rph] | |
| RA | 3,917,011 | T→C | N122S (AAC→AGC) | atpD ← | F1 sector of membrane‑bound ATP synthase, beta subunit |
| RA | 3,928,131 | T→C | V326A (GTC→GCC) | asnA → | asparagine synthetase A |
| RA | 4,135,739 | T→C | V635V (GTT→GTC) | katG → | catalase‑peroxidase HPI, heme b‑containing |
| RA | 4,136,037 | C→T | intergenic (+22/‑71) | katG → / → yijE | catalase‑peroxidase HPI, heme b‑containing/EamA‑like transporter family protein |
| RA | 4,183,258 | G→A | E672K (GAA→AAA) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,282,608 | A→G | G156G (GGT→GGC) | yjcF ← | pentapeptide repeats protein |
| RA | 4,283,250 | A→G | intergenic (‑175/+3) | yjcF ← / ← actP | pentapeptide repeats protein/acetate transporter |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,397,649 | Δ1 bp | coding (238/1848 nt) | mutL → | methyl‑directed mismatch repair protein |
| RA | 4,438,767 | C→T | A166T (GCG→ACG) | ytfJ ← | putative transcriptional regulator |
| RA | 4,451,758 | A→G | Q234R (CAG→CGG) | ytfR → | putative sugar ABC transporter ATPase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423699–3424234 | 3424568–3424238 | 5–870 | 55 [50] | [53] 55 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 257907 | 0 (0.000) | 95 (0.990) | 69/182 | 0.2 | 100% | intergenic (+8/‑769) | 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 | 258684 = | 0 (0.000) | pseudogene (9/331 nt) | crl | 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 | 1207790 = | 9 (0.090) | 69 (0.790) | 50/166 | 0.9 | 91.1% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 6 (0.070) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 9 (0.090) | 75 (0.860) | 50/166 | 0.9 | 91.7% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 6 (0.070) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 112 (1.120) | 84/190 | 0.0 | 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) | 86 (0.900) | 63/182 | 0.4 | 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 | |||||