mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.29.0 revision 8f9c342918e4
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 11,664 | A→C | D41E (GAT→GAG) | yaaI ← | UPF0412 family protein |
| RA | 52,332 | A→C | I33M (ATT→ATG) | rsmA ← | 16S rRNA m(6)A1518, m(6)A1519 dimethyltransferase, SAM‑dependent |
| RA | 83,066 | A→C | V155G (GTC→GGC) | leuA ← | 2‑isopropylmalate synthase |
| RA | 111,300 | T→C | L86P (CTG→CCG) | mutT → | dGTP‑preferring nucleoside triphosphate pyrophosphohydrolase |
| RA | 112,052 | T→G | K183T (AAA→ACA) | zapD ← | FtsZ stabilizer |
| RA | 156,869 | T→G | L5F (TTA→TTC) | yadN ← | putative fimbrial‑like adhesin protein |
| RA | 206,330 | T→G | F402C (TTC→TGC) | dnaE → | DNA polymerase III alpha subunit |
| RA | 257,250 | A→C | T242P (ACC→CCC) | frsA → | fermentation‑respiration switch protein; PTS Enzyme IIA(Glc)‑binding protein; pNP‑butyrate esterase activity |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 301,521 | A→C | Y123D (TAC→GAC) | paoB ← | PaoABC aldehyde oxidoreductase, FAD‑containing subunit |
| RA | 457,616 | T→G | L64R (CTA→CGA) | clpX → | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease |
| RA | 473,636 | T→G | F224C (TTC→TGC) | amtB → | ammonium transporter |
| RA | 511,572 | A→C | intergenic (‑193/‑69) | copA ← / → glsA | copper transporter/glutaminase 1 |
| RA | 587,023 | A→C | intergenic (‑115/+68) | envY ← / ← ybcH | porin thermoregulatory transcriptional activator/PRK09936 family protein |
| RA | 622,725 | A→C | E142D (GAA→GAC) | entS → | enterobactin exporter, iron‑regulated |
| RA | 679,800 | A→C | Y98S (TAT→TCT) | ybeU → | DUF1266 family protein |
| RA | 701,839 | T→G | T305P (ACG→CCG) | nagA ← | N‑acetylglucosamine‑6‑phosphate deacetylase |
| RA | 758,662 | A→C | intergenic (+257/‑44) | sdhB → / → sucA | succinate dehydrogenase, FeS subunit/2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding |
| RA | 798,070 | A→C | V121G (GTC→GGC) | ybhA ← | pyridoxal phosphate (PLP) phosphatase |
| RA | 903,504 | A→C | I77M (ATT→ATG) | artP ← | arginine ABC transporter ATPase |
| RA | 977,748 | T→G | F475V (TTT→GTT) | mukB → | chromosome condensin MukBEF, ATPase and DNA‑binding subunit |
| RA | 1,040,032 | T→G | L246R (CTG→CGG) | cbdB → | cytochrome bd‑II oxidase, subunit II |
| RA | 1,113,464 | T→G | intergenic (+58/‑115) | opgH → / → yceK | OPG biosynthetic ACP‑dependent transmembrane UDP‑glucose beta‑1,2 glycosyltransferase; nutrient‑dependent cell size regulator, FtsZ assembly antagonist/outer membrane integrity lipoprotein |
| RA | 1,133,542 | A→C | E323D (GAA→GAC) | flgE → | flagellar hook protein |
| RA | 1,188,512 | A→C | L422* (TTA→TGA) | phoQ ← | sensory histidine kinase in two‑component regulatory system with PhoP |
| RA | 1,196,220 | C→T | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,232 | C→T | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,245 | T→C | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,247 | A→G | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,221,238 | T→G | pseudogene (1638/2574 nt) | ycgH → | pseudogene; putative ATP‑binding component of a transport system |
| RA | 1,335,050 | T→G | intergenic (+221/‑74) | cysB → / → ymiA | N‑acetylserine‑responsive cysteine regulon transcriptional activator; autorepressor/uncharacterized protein |
| RA | 1,348,890 | A→C | L8R (CTA→CGA) | rnb ← | ribonuclease II |
| RA | 1,353,128 | C→A | V167V (GTG→GTT) | sapD ← | antimicrobial peptide ABC transporter ATPase |
| RA | 1,367,147 | T→G | K256Q (AAA→CAA) | pspF ← | psp operon transcriptional activator |
| RA | 1,440,960 | A→C | intergenic (‑176/‑98) | pfo ← / → ydbJ | pyruvate‑flavodoxin oxidoreductase/DUF333 family putative lipoprotein |
| RA | 1,459,435 | A→C | I128L (ATT→CTT) | paaH → | 3‑hydroxyadipyl‑CoA dehydrogenase, NAD+‑dependent |
| RA | 1,526,968 | T→G | L10R (CTC→CGC) | yncH → | IPR020099 family protein |
| RA | 1,637,726 | (T)8→7 | coding (57/174 nt) | gnsB ← | Qin prophage; multicopy suppressor of secG(Cs) and fabA6(Ts) |
| RA | 1,666,363 | T→G | I350S (ATT→AGT) | clcB → | H(+)/Cl(‑) exchange transporter |
| RA | 1,698,747 | A→C | I145S (ATC→AGC) | malI ← | transcriptional repressor of Mal regulon |
| RA | 1,703,763 | A→C | L182L (CTT→CTG) | ydgJ ← | putative oxidoreductase |
| RA | 1,724,722 | A→C | intergenic (‑67/+14) | sodC ← / ← ydhF | superoxide dismutase, Cu, Zn, periplasmic/putative oxidoreductase |
| RA | 1,736,425 | T→G | N289T (AAT→ACT) | ydhP ← | putative MFS transporter, inner membrane protein |
| RA | 1,814,762 | A→C | K299T (AAA→ACA) | katE → | catalase HPII, heme d‑containing |
| RA | 1,840,197 | T→G | L244R (CTT→CGT) | ynjE → | molybdopterin synthase sulfurtransferase |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| 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 |
| JC | 2,804,835 | Δ7 bp | coding (21‑27/1203 nt) | proV → | glycine betaine/proline ABC transporter periplasmic binding protein |
| RA | 2,879,197 | T→G | E192D (GAA→GAC) | ygbT ← | multifunctional endonuclease Cas1, CRISPR adaptation protein; DNA repair enzyme |
| RA | 2,894,532 | T→G | S113A (TCA→GCA) | ygcP → | putative antiterminator regulatory protein |
| RA | 2,904,323 | T→G | intergenic (+949/+424) | ygcE → / ← queE | putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis |
| RA | 2,924,700 | T→G | intergenic (‑587/+35) | yqcC ← / ← syd | DUF446 family protein/SecY‑interacting protein |
| RA | 2,955,480 | A→C | L175R (CTG→CGG) | recB ← | exonuclease V (RecBCD complex), beta subunit |
| RA | 2,964,902 | T→G | D85A (GAT→GCT) | thyA ← | thymidylate synthetase |
| RA | 3,035,568 | A→C | D213E (GAT→GAG) | prfB ← | peptide chain release factor RF‑2 |
| RA | 3,084,656 | T→G | E419A (GAA→GCA) | speA ← | biosynthetic arginine decarboxylase, PLP‑binding |
| RA | 3,111,465 | A→C | pseudogene (626/963 nt) | yghE ← | pseudogene, secretion pathway protein, L‑type protein homology; putative general secretion pathway for protein export (GSP) |
| RA | 3,182,139 | T→G | Q90P (CAG→CCG) | ygiD ← | 4,5‑ DOPA‑extradiol‑dioxygenase |
| RA | 3,213,290 | C→A | Q82K (CAG→AAG) | rpoD → | RNA polymerase, sigma 70 (sigma D) factor |
| RA | 3,219,912 | A→C | K140T (AAA→ACA) | patA → | putrescine:2‑oxoglutaric acid aminotransferase, PLP‑dependent |
| RA | 3,239,097 | T→G | L173R (CTG→CGG) | alx → | putative membrane‑bound redox modulator |
| RA | 3,247,589 | T→G | intergenic (+161/‑184) | exuR → / → yqjA | hexuronate regulon transcriptional repressor; autorepressor/general envelope maintenance protein; DedA family inner membrane protein; putative multidrug efflux transporter |
| RA | 3,281,717 | A→C | intergenic (+92/‑259) | agaA → / → agaS | pseudogene, N‑acetylgalactosamine‑6‑phosphate deacetylase fragment; putative N‑acetylgalactosamine‑6‑phosphate deacetylase/tagatose‑6‑phosphate ketose/aldose isomerase |
| RA | 3,331,811 | T→G | K309Q (AAG→CAG) | yhbE ← | EamA family inner membrane putative transporter |
| RA | 3,348,462 | T→G | L4* (TTA→TGA) | yrbL → | Mg(2+)‑starvation‑stimulated protein |
| RA | 3,349,078 | A→C | E209D (GAA→GAC) | yrbL → | Mg(2+)‑starvation‑stimulated protein |
| RA | 3,400,966 | A→C | I41S (ATT→AGT) | mreB ← | cell wall structural complex MreBCD, actin‑like component MreB |
| 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 |
| RA | 3,582,141 | T→G | N93K (AAT→AAG) | yhhZ → | putative Hcp1 family polymorphic toxin protein; putative colicin‑like DNase/tRNase activity |
| RA | 3,614,957 | A→C | S431R (AGT→CGT) | nikA → | nickel/heme ABC transporter periplasmic binding protein |
| RA | 3,691,406 | T→G | D401A (GAT→GCT) | bcsB ← | regulator of cellulose synthase, cyclic di‑GMP binding |
| MC JC | 3,815,859 | Δ82 bp | [rph]–[rph] | [rph], [rph] | |
| RA | 3,823,987 | G→T | G530C (GGT→TGT) | spoT → | bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase |
| RA | 3,854,965 | C→G | G348G (GGC→GGG) | emrD → | multidrug efflux system protein |
| RA | 3,891,019 | T→G | S262A (TCC→GCC) | tnaB → | tryptophan transporter of low affinity |
| RA | 3,903,374 | A→C | F110V (TTT→GTT) | bglB ← | cryptic phospho‑beta‑glucosidase B |
| RA | 4,003,860 | A→C | F107V (TTT→GTT) | rarD ← | putative chloramphenical resistance permease |
| RA | 4,133,696 | A→C | intergenic (+190/‑139) | metF → / → katG | 5,10‑methylenetetrahydrofolate reductase/catalase‑peroxidase HPI, heme b‑containing |
| RA | 4,143,217 | A→C | M230L (ATG→CTG) | frwC → | putative enzyme IIC component of PTS |
| RA | 4,256,722 | A→C | E29A (GAA→GCA) | dgkA → | diacylglycerol kinase |
| RA | 4,272,717 | A→C | Y385* (TAT→TAG) | uvrA ← | ATPase and DNA damage recognition protein of nucleotide excision repair excinuclease UvrABC |
| RA | 4,290,993 | A→C | Y173S (TAT→TCT) | nrfD → | formate‑dependent nitrite reductase, membrane subunit |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,304,847 | T→G | N584T (AAC→ACC) | yjcS ← | metallo‑beta‑lactamase superfamily protein |
| RA | 4,321,045 | A→C | L68* (TTA→TGA) | phnH ← | ribophosphonate triphosphate synthase subunit |
| RA | 4,369,961 | A→C | I151S (ATT→AGT) | yjeH ← | putative transporter |
| RA | 4,372,620 | A→C | L532F (TTA→TTC) | groL → | Cpn60 chaperonin GroEL, large subunit of GroESL |
| RA | 4,416,967 | T→G | S6A (TCA→GCA) | yjfP → | acyl CoA esterase |
| RA | 4,469,328 | T→G | L568L (CTT→CTG) | mgtA → | magnesium transporter |
| RA | 4,494,164 | T→G | E81D (GAA→GAC) | idnD ← | L‑idonate 5‑dehydrogenase, NAD‑binding |
| RA | 4,494,308 | T→G | Q33H (CAA→CAC) | idnD ← | L‑idonate 5‑dehydrogenase, NAD‑binding |
| RA | 4,509,433 | A→C | pseudogene (425/471 nt) | insO → | pseudogene, IS911 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,623,272 | A→C | F282L (TTT→TTG) | lplA ← | lipoate‑protein ligase A |
| RA | 4,626,686 | A→C | N259H (AAC→CAC) | radA → | DNA repair protein |
| RA | 4,628,246 | A→C | D311A (GAT→GCT) | nadR → | trifunctional protein: nicotinamide mononucleotide adenylyltransferase, ribosylnicotinamide kinase, transcriptional repressor |
| RA | 4,636,416 | T→G | F137C (TTT→TGT) | creB → | response regulator in two‑component regulatory system with CreC |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196262 | 1211479 | 15218 | 46 [44] | [44] 45 | [icd]–[icdC] | 25 genes [icd], ymfD, ymfE, lit, intE, xisE, ymfI, ymfJ, cohE, croE, ymfL, ymfM, oweE, aaaE, ymfR, beeE, jayE, ymfQ, stfP, tfaP, tfaE, stfE, pinE, mcrA, [icdC] |
| * | * | ÷ | NC_000913 | 3423734–3424234 | 3424569–3424238 | 5–836 | 45 [44] | [44] 45 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 70 (0.870) | 61/290 | 0.5 | 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 | |||||