mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 53,376 | G→A | 8.8% | P14L (CCC→CTC) | pdxA ← | 4‑hydroxy‑L‑threonine phosphate dehydrogenase, NAD‑dependent |
| RA | 53,379 | T→C | 7.3% | E13G (GAG→GGG) | pdxA ← | 4‑hydroxy‑L‑threonine phosphate dehydrogenase, NAD‑dependent |
| RA | 217,587 | G→A | 6.0% | P397S (CCG→TCG) | proS ← | prolyl‑tRNA synthetase |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 301,767 | C→T | 5.1% | E41K (GAA→AAA) | paoB ← | PaoABC aldehyde oxidoreductase, FAD‑containing subunit |
| RA | 370,186 | C→T | 7.6% | Q526* (CAA→TAA) | mhpA → | 3‑(3‑hydroxyphenyl)propionate hydroxylase |
| RA | 413,124 | A→T | 5.3% | V877D (GTT→GAT) | sbcC ← | exonuclease, dsDNA, ATP‑dependent |
| RA | 574,486:1 | +C | 6.0% | intergenic (+147/+43) | quuD → / ← nmpC | DLP12 prophage; putative antitermination protein/DLP12 prophage; truncated outer membrane porin (pseudogene);IS, phage, Tn; Phage or Prophage Related; outer membrane porin protein; locus of qsr prophage |
| RA | 574,494 | A→G | 5.4% | intergenic (+155/+35) | quuD → / ← nmpC | DLP12 prophage; putative antitermination protein/DLP12 prophage; truncated outer membrane porin (pseudogene);IS, phage, Tn; Phage or Prophage Related; outer membrane porin protein; locus of qsr prophage |
| RA | 574,504 | Δ1 bp | 5.3% | intergenic (+165/+25) | quuD → / ← nmpC | DLP12 prophage; putative antitermination protein/DLP12 prophage; truncated outer membrane porin (pseudogene);IS, phage, Tn; Phage or Prophage Related; outer membrane porin protein; locus of qsr prophage |
| RA | 651,030 | C→T | 5.5% | R276H (CGC→CAC) | citC ← | citrate lyase ligase; [citrate [pro‑3S]‑lyase] ligase |
| RA | 743,396 | T→C | 5.8% | F190F (TTT→TTC) | ybgI → | NIF3 family metal‑binding protein |
| RA | 788,967 | C→T | 6.8% | G338D (GGC→GAC) | galK ← | galactokinase |
| RA | 845,575 | G→A | 5.4% | intergenic (‑95/+166) | ybiO ← / ← glnQ | mechanosensitive channel protein, intermediate conductance/glutamine transporter subunit |
| RA | 845,576 | G→C | 5.4% | intergenic (‑96/+165) | ybiO ← / ← glnQ | mechanosensitive channel protein, intermediate conductance/glutamine transporter subunit |
| RA | 845,577 | G→C | 5.1% | intergenic (‑97/+164) | ybiO ← / ← glnQ | mechanosensitive channel protein, intermediate conductance/glutamine transporter subunit |
| RA | 845,578 | T→C | 5.4% | intergenic (‑98/+163) | ybiO ← / ← glnQ | mechanosensitive channel protein, intermediate conductance/glutamine transporter subunit |
| RA | 851,934 | Δ1 bp | 5.1% | coding (664/1584 nt) | opgE ← | OPG biosynthetic transmembrane phosphoethanolamine transferase |
| RA | 886,431 | G→A | 6.1% | S303S (AGC→AGT) | ybjJ ← | putative drug efflux MFS transporter, inner membrane protein |
| RA | 900,191 | T→A | 5.0% | I129F (ATT→TTT) | artJ ← | arginine ABC transporter periplasmic binding protein |
| RA | 1,231,052 | G→A | 5.5% | V96M (GTG→ATG) | umuD → | translesion error‑prone DNA polymerase V subunit; RecA‑activated auto‑protease |
| RA | 1,235,686 | A→G | 9.1% | intergenic (+29/+23) | fadR → / ← ycgB | fatty acid metabolism regulon transcriptional regulator/SpoVR family stationary phase protein |
| RA | 1,235,687 | A→T | 9.0% | intergenic (+30/+22) | fadR → / ← ycgB | fatty acid metabolism regulon transcriptional regulator/SpoVR family stationary phase protein |
| RA | 1,235,688 | A→T | 9.1% | intergenic (+31/+21) | fadR → / ← ycgB | fatty acid metabolism regulon transcriptional regulator/SpoVR family stationary phase protein |
| RA | 1,235,689 | C→T | 9.2% | intergenic (+32/+20) | fadR → / ← ycgB | fatty acid metabolism regulon transcriptional regulator/SpoVR family stationary phase protein |
| RA | 1,265,851 | T→C | 5.6% | A280A (GCT→GCC) | prfA → | peptide chain release factor RF‑1 |
| 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 | 1,504,893 | G→A | 6.8% | intergenic (+28/+12) | insQ → / ← ydcO | IS609 transposase B/BenE family inner membrane putative transporter |
| RA | 1,534,406 | A→G | 5.3% | Q128R (CAG→CGG) | nhoA → | N‑hydroxyarylamine O‑acetyltransferase |
| RA | 1,686,586 | C→A | 8.0% | M1M (ATG→ATT) † | fumC ← | fumarate hydratase (fumarase C),aerobic Class II |
| RA | 1,698,585 | T→G | 5.5% | E199A (GAA→GCA) | malI ← | transcriptional repressor of Mal regulon |
| RA | 1,698,587 | T→A | 5.5% | A198A (GCA→GCT) ‡ | malI ← | transcriptional repressor of Mal regulon |
| RA | 1,698,589 | C→A | 6.2% | A198S (GCA→TCA) ‡ | malI ← | transcriptional repressor of Mal regulon |
| RA | 1,701,108 | A→T | 5.4% | N51I (AAT→ATT) | malY → | PLP‑dependent beta‑cystathionase and maltose regulon regulator |
| RA | 1,736,692 | C→T | 5.5% | R200H (CGT→CAT) | ydhP ← | putative MFS transporter, inner membrane protein |
| RA | 1,806,340 | C→T | 100% | intergenic (‑257/‑30) | ydiY ← / → pfkB | acid‑inducible putative outer membrane protein/6‑phosphofructokinase II |
| JC | 1,806,703 | Δ3 bp | 8.1% | coding (334‑336/930 nt) | pfkB → | 6‑phosphofructokinase II |
| RA | 1,806,964 | C→G | 7.0% | L199V (CTC→GTC) | pfkB → | 6‑phosphofructokinase II |
| RA | 1,806,974 | C→T | 18.0% | P202L (CCG→CTG) | pfkB → | 6‑phosphofructokinase II |
| RA | 1,807,103 | C→A | 65.8% | P245Q (CCG→CAG) | pfkB → | 6‑phosphofructokinase II |
| RA | 1,807,286 | A→C | 15.1% | Y306S (TAC→TCC) | pfkB → | 6‑phosphofructokinase II |
| RA | 1,810,062 | T→C | 7.3% | intergenic (+14/‑149) | yniC → / → ydjM | 2‑deoxyglucose‑6‑P phosphatase/inner membrane protein regulated by LexA |
| RA | 1,810,065 | T→G | 6.7% | intergenic (+17/‑146) | yniC → / → ydjM | 2‑deoxyglucose‑6‑P phosphatase/inner membrane protein regulated by LexA |
| RA | 1,810,069 | G→A | 7.2% | intergenic (+21/‑142) | yniC → / → ydjM | 2‑deoxyglucose‑6‑P phosphatase/inner membrane protein regulated by LexA |
| RA | 1,819,614 | C→T | 5.2% | A64A (GCG→GCA) | chbA ← | N,N'‑diacetylchitobiose‑specific enzyme IIA component of PTS |
| RA | 1,837,799 | G→A | 5.6% | A196A (GCG→GCA) | ynjC → | putative ABC transporter permease |
| RA | 1,863,802 | C→A | 6.0% | intergenic (+36/‑48) | gapA → / → yeaD | glyceraldehyde‑3‑phosphate dehydrogenase A/D‑hexose‑6‑phosphate epimerase‑like protein |
| RA | 1,864,763 | A→T | 5.7% | intergenic (+29/+19) | yeaD → / ← yeaE | D‑hexose‑6‑phosphate epimerase‑like protein/aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent |
| RA | 1,864,768 | T→C | 5.1% | intergenic (+34/+14) | yeaD → / ← yeaE | D‑hexose‑6‑phosphate epimerase‑like protein/aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent |
| 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 | 2,022,388 | T→A | 5.9% | Y174N (TAC→AAC) | fliP → | flagellar biosynthesis protein |
| RA | 2,028,158 | G→C | 7.1% | intergenic (‑141/+30) | yedQ ← / ← yodC | putative membrane‑anchored diguanylate cyclase/uncharacterized protein |
| RA | 2,028,160 | G→C | 7.1% | intergenic (‑143/+28) | yedQ ← / ← yodC | putative membrane‑anchored diguanylate cyclase/uncharacterized protein |
| RA | 2,091,507 | G→T | 5.3% | P137P (CCG→CCT) | hisD → | bifunctional histidinal dehydrogenase/ histidinol dehydrogenase |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,147,417 | C→T | 6.2% | G42S (GGC→AGC) | alkA ← | 3‑methyl‑adenine DNA glycosylase II |
| 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 |
| RA | 2,305,085 | A→G | 9.8% | intergenic (+692/+23) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,305,086 | C→G | 9.8% | intergenic (+693/+22) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,305,087 | C→T | 9.8% | intergenic (+694/+21) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,353,935 | G→A | 5.9% | R430H (CGT→CAT) | glpA → | anaerobic sn‑glycerol‑3‑phosphate dehydrogenase, large FAD/NAD(P)‑binding subunit |
| RA | 2,497,023 | A→T | 5.4% | intergenic (+31/+34) | ypdK → / ← alaC | inner membrane protein/glutamate‑pyruvate aminotransferase; glutamic‑pyruvic transaminase (GPT); alanine transaminase |
| RA | 2,497,024 | T→G | 5.4% | intergenic (+32/+33) | ypdK → / ← alaC | inner membrane protein/glutamate‑pyruvate aminotransferase; glutamic‑pyruvic transaminase (GPT); alanine transaminase |
| RA | 2,497,025 | C→A | 5.2% | intergenic (+33/+32) | ypdK → / ← alaC | inner membrane protein/glutamate‑pyruvate aminotransferase; glutamic‑pyruvic transaminase (GPT); alanine transaminase |
| RA | 2,497,026 | A→T | 5.3% | intergenic (+34/+31) | ypdK → / ← alaC | inner membrane protein/glutamate‑pyruvate aminotransferase; glutamic‑pyruvic transaminase (GPT); alanine transaminase |
| RA | 2,676,245 | C→T | 5.6% | R194H (CGC→CAC) | yphD ← | putative sugar ABC transporter permease |
| RA | 2,691,169 | A→T | 7.0% | noncoding (172/184 nt) | glmY ← | sRNA activator of glmS mRNA, glmZ processing antagonist |
| RA | 2,691,171 | T→A | 6.6% | noncoding (170/184 nt) | glmY ← | sRNA activator of glmS mRNA, glmZ processing antagonist |
| RA | 2,691,173 | A→T | 6.9% | noncoding (168/184 nt) | glmY ← | sRNA activator of glmS mRNA, glmZ processing antagonist |
| RA | 2,793,741 | T→C | 5.2% | L336P (CTG→CCG) | gabT → | 4‑aminobutyrate aminotransferase, PLP‑dependent |
| RA | 2,851,218 | G→A | 5.0% | S73N (AGC→AAC) | hypB → | GTP hydrolase involved in nickel liganding into hydrogenases |
| RA | 3,020,252 | A→T | 5.4% | E364D (GAA→GAT) | ssnA → | putative chlorohydrolase/aminohydrolase |
| RA | 3,180,497 | Δ1 bp | 6.5% | coding (77/1161 nt) | ygiC → | ATP‑Grasp family ATPase |
| RA | 3,213,488 | T→C | 6.2% | Y148H (TAC→CAC) | rpoD → | RNA polymerase, sigma 70 (sigma D) factor |
| RA | 3,270,030 | T→C | 11.9% | intergenic (+428/+186) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,372,596 | G→A | 5.3% | intergenic (‑22/+87) | nanT ← / ← nanA | sialic acid transporter/N‑acetylneuraminate lyase |
| RA | 3,374,901 | A→T | 5.7% | L11F (TTA→TTT) | dcuD → | putative transporter |
| RA | 3,424,646 | C→A | 8.0% | noncoding (2138/2904 nt) | rrlD ← | 23S ribosomal RNA of rrnD operon |
| RA | 3,424,661 | C→A | 9.2% | noncoding (2123/2904 nt) | rrlD ← | 23S ribosomal RNA of rrnD operon |
| 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 |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| MC JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,080,616 | C→A | 7.5% | G205C (GGC→TGC) | fdhE ← | formate dehydrogenase formation protein |
| RA | 4,080,621 | T→G | 7.8% | Q203P (CAA→CCA) | fdhE ← | formate dehydrogenase formation protein |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,234,855 | C→T | 5.4% | N366N (AAC→AAT) | pgi → | glucosephosphate isomerase |
| RA | 4,296,060 | C→T | 23.1% | 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 | 4,439,845 | T→A | 7.3% | intergenic (+52/+27) | ytfK → / ← ytfL | DUF1107 family protein/UPF0053 family inner membrane protein |
| RA | 4,545,568 | T→C | 7.6% | L158P (CTG→CCG) | fimD → | fimbrial usher outer membrane porin protein; FimCD chaperone‑usher |
| RA | 4,606,239 | A→G | 15.4% | noncoding (48/87 nt) | leuP ← | tRNA‑Leu |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 2066239–2066619 | 2066619 | 1–381 | 39 [35] | [35] 36 | [insH1] | [insH1] |
| * | * | ÷ | NC_000913 | 3423747–3424234 | 3424532–3424238 | 5–786 | 37 [35] | [35] 36 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 4107529 | 4108519 | 991 | 37 [35] | [35] 38 | pfkA | pfkA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 288405 = | 75 (0.820) | 4 (0.050) | 4/242 | NT | 5.6% | coding (758/759 nt) | yagI | CP4‑6 prophage; putative DNA‑binding transcriptional regulator |
| ? | NC_000913 | 288449 = | 64 (0.760) | coding (714/759 nt) | yagI | CP4‑6 prophage; putative DNA‑binding transcriptional regulator | |||||
| * | ? | NC_000913 | 332801 = | 85 (0.930) | 5 (0.060) | 5/252 | NT | 6.1% | coding (431/1089 nt) | yahA | c‑di‑GMP‑specific phosphodiesterase |
| ? | NC_000913 | 332841 = | 72 (0.820) | coding (471/1089 nt) | yahA | c‑di‑GMP‑specific phosphodiesterase | |||||
| * | ? | NC_000913 | 1207790 = | 33 (0.360) | 29 (0.360) | 26/228 | NT | 46.1% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 39 (0.490) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 30 (0.330) | 29 (0.360) | 24/228 | NT | 47.0% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 39 (0.490) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1396531 = | NA (NA) | 3 (0.030) | 3/248 | NT | NA | noncoding (488/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 1428264 | NA (NA) | noncoding (531/1196 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 1411899 = | 114 (1.250) | 26 (0.360) | 21/208 | NT | 23.4% | coding (50/936 nt) | ttcA | tRNA s(2)C32 thioltransferase, iron sulfur cluster protein |
| ? | NC_000913 | = 1434958 | 79 (1.090) | pseudogene (51/51 nt) | ttcC | pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1757141 = | 90 (0.990) | 5 (0.060) | 5/244 | NT | 5.7% | intergenic (+31/‑280) | pykF/lpp | pyruvate kinase I/murein lipoprotein |
| ? | NC_000913 | 1757161 = | 80 (0.940) | intergenic (+51/‑260) | pykF/lpp | pyruvate kinase I/murein lipoprotein | |||||
| * | ? | NC_000913 | 2236520 = | NA (NA) | 3 (0.040) | 3/240 | NT | NA | intergenic (+20/+223) | preA/mglC | dihydropyrimidine dehydrogenase, NADH‑dependent, subunit C/methyl‑galactoside transporter subunit |
| ? | NC_000913 | 2236534 = | NA (NA) | noncoding (1/150 nt) | REP156 (repetitive extragenic palindromic) element; contains 3 REP sequences | REP156 (repetitive extragenic palindromic) element; contains 3 REP sequences | |||||
| * | ? | NC_000913 | = 2539674 | NA (NA) | 3 (0.030) | 3/246 | NT | NA | intergenic (‑91/+43) | cysM/cysA | cysteine synthase B (O‑acetylserine sulfhydrolase B)/sulfate/thiosulfate transporter subunit |
| ? | NC_000913 | = 2539688 | NA (NA) | intergenic (‑105/+29) | cysM/cysA | cysteine synthase B (O‑acetylserine sulfhydrolase B)/sulfate/thiosulfate transporter subunit | |||||
| * | ? | NC_000913 | = 4168341 | 36 (0.400) | 5 (0.060) | 5/240 | NT | 12.6% | intergenic (+141/‑31) | rrsB/gltT | 16S ribosomal RNA of rrnB operon/tRNA‑Glu |
| ? | NC_000913 | = 4168363 | 36 (0.430) | intergenic (+163/‑9) | rrsB/gltT | 16S ribosomal RNA of rrnB operon/tRNA‑Glu | |||||
| * | ? | NC_000913 | 4542682 = | 124 (1.360) | 6 (0.070) | 6/242 | NT | 5.1% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | 4542996 = | 106 (1.250) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||