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
MC JC 257,908 Δ776 bp 100% [crl] [crl]
RA 451,643 G→A 76.7% intergenic (‑33/+427) cyoA ← / ← ampG cytochrome o ubiquinol oxidase subunit II/muropeptide transporter
RA 652,453 G→A 5.4% A73A (GCG→GCA citA → sensory histidine kinase in two‑component regulatory system with CitB
RA 779,226 Δ1 bp 4.4% coding (160/522 nt) pal → peptidoglycan‑associated outer membrane lipoprotein
RA 970,421 C→T 4.9% R345C (CGC→TGC)  ycaQ → DUF1006 family protein with C‑terminal wHTH domain
RA 989,521 C→A 4.4% G279V (GGC→GTC)  pncB ← nicotinate phosphoribosyltransferase
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 1,708,662 C→G 6.9% Q582E (CAA→GAA)  rsxC → SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex
RA 1,708,844 C→G 14.1% A642A (GCC→GCG rsxC → SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex
RA 1,708,847 G→A 11.4% E643E (GAG→GAA rsxC → SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex
RA 1,902,141 G→A 5.2% G32S (GGC→AGC)  manX → fused mannose‑specific PTS enzymes: IIA component/IIB component
MC JC 1,978,503 Δ776 bp 100% insB1insA insB1, insA
RA 2,132,787 A→C 100% I204S (ATC→AGC)  wcaA ← putative glycosyl transferase
RA 2,202,094 G→A 8.8% A606A (GCG→GCA yehI → DUF4132 domain‑containing protein
RA 2,241,662:1 +A 5.1% coding (5/1041 nt) galS ← galactose‑ and fucose‑inducible galactose regulon transcriptional isorepressor, mgl operon transcriptional repressor, autorepressor
RA 2,304,678 T→C 9.5% intergenic (+287/+428) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,649,036 A→C 4.2% F1084V (TTT→GTT)  yfhM ← bacterial alpha2‑macroglobulin colonization factor ECAM, anti‑host protease defense factor, periplasmic inner membrane‑anchored lipoprotein
RA 2,854,256 A→T 4.9% I335I (ATA→ATT hypE → carbamoyl dehydratase, hydrogenases 1,2,3 maturation protein
RA 3,065,954 A→G 8.3% E385E (GAA→GAG scpC → propionyl‑CoA:succinate CoA transferase
RA 3,339,606 G→C 3.2% A153G (GCA→GGA)  mlaF ← ABC transporter maintaining OM lipid asymmetry, ATP‑binding protein
MC JC 3,815,858 Δ82 bp 100% [rph][rph] [rph], [rph]
RA 3,951,535 Δ1 bp 100% pseudogene (977/984 nt) ilvG → pseudogene, acetolactate synthase 2 large subunit, valine‑insensitive, acetolactate synthase II, large subunit, cryptic, interrupted
RA 3,951,597:1 +A 6.0% pseudogene (57/663 nt) ilvG → pseudogene, acetolactate synthase 2 large subunit, valine‑insensitive, acetolactate synthase II, large subunit, cryptic, interrupted
JC 3,968,507 Δ12 bp 10.8% coding (593‑604/1104 nt) wecA → UDP‑GlcNAc:undecaprenylphosphate GlcNAc‑1‑phosphate transferase
JC 3,968,670 Δ9 bp 5.4% coding (756‑764/1104 nt) wecA → UDP‑GlcNAc:undecaprenylphosphate GlcNAc‑1‑phosphate transferase
MC JC 4,001,644 Δ5 bp 100% coding (220‑224/951 nt) corA → magnesium/nickel/cobalt transporter
RA 4,012,601 A→T 3.2% V72E (GTA→GAA)  metR ← methionine biosynthesis regulon transcriptional regulator
RA 4,146,260 A→G 3.2% D756G (GAC→GGC) 
T2A (ACA→GCA) 
pflD →
pflC →
putative glycine radical domain‑containing pyruvate formate‑lyase
putative [formate‑C‑acetyltransferase 2]‑activating enzyme, pyruvate formate‑lyase 1‑activating enzyme
RA 4,184,542 C→A 100% P1100Q (CCG→CAG)  rpoB → RNA polymerase, beta subunit
RA 4,274,207 C→T 3.7% G28G (GGC→GGT ssb → single‑stranded DNA‑binding protein
RA 4,296,189 A→G 34.1% intergenic (+396/+248) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,190 A→C 45.0% intergenic (+397/+247) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,267 T→C 9.3% intergenic (+474/+170) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,544,445 T→C 9.3% Y47Y (TAT→TAC fimC → periplasmic chaperone
RA 4,565,628 C→T 4.6% R75H (CGC→CAC)  yjiM ← putative 2‑hydroxyglutaryl‑CoA dehydratase

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 2469042 2469912 871 23 [21] [21] 22 [gtrB]–[gtrS] [gtrB], [gtrS]
* * ÷ NC_000913 2785996 2786710 715 22 [20] [21] 23 [ygaQ] [ygaQ]
* * ÷ NC_000913 2994959 2995475 517 23 [21] [20] 25 [ygeK]–[ygeN] [ygeK], [ygeN]
* * ÷ NC_000913 3287074 3287427 354 23 [21] [19] 23 [yraH] [yraH]
* * ÷ NC_000913 3360767 3361277 511 23 [21] [21] 23 [gltF] [gltF]
* * ÷ NC_000913 3423895–3424229 3424394–3424237 9–500 22 [20] [20] 22 rrlD 23S ribosomal RNA of rrnD operon
* * ÷ NC_000913 3581680 3582197 518 24 [18] [20] 22 [yhhZ] [yhhZ]
* * ÷ NC_000913 3769553 3770077 525 22 [20] [17] 23 [yibV]–[yibU] [yibV], yibV, yibU, [yibU]
* * ÷ NC_000913 3798635 3799652 1018 23 [21] [19] 22 [waaU]–[waaZ] [waaU], [waaZ]
* * ÷ NC_000913 4268444 4268724 281 22 [21] [21] 25 tyrB/yjbS tyrosine aminotransferase, tyrosine‑repressible, PLP‑dependent/uncharacterized protein

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 224910 =NA (NA)5 (0.060) 4/498 NT NA noncoding (1140/1542 nt) rrsH 16S ribosomal RNA of rrnH operon
?NC_000913 225157 = NA (NA)noncoding (1387/1542 nt) rrsH 16S ribosomal RNA of rrnH operon
* ? NC_000913 = 23179172 (0.910)3 (0.040) 3/506 NT 3.6% coding (670/801 nt) yafD endo/exonuclease/phosphatase family protein
?NC_000913 = 231901 91 (1.160)coding (780/801 nt) yafD endo/exonuclease/phosphatase family protein
* ? NC_000913 = 24300991 (1.140)5 (0.060) 3/500 NT 5.1% coding (295/2445 nt) fadE acyl coenzyme A dehydrogenase
?NC_000913 = 243192 96 (1.240)coding (112/2445 nt) fadE acyl coenzyme A dehydrogenase
* ? NC_000913 257908 =NA (NA)56 (0.700) 43/514 NT 100% 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 0 (0.000)intergenic (‑117/‑488) hns/tdk global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
* ? NC_000913 379965 =52 (0.650)4 (0.050) 4/504 NT 6.8% intergenic (‑84/+104) frmR/yaiO regulator protein that represses frmRAB operon/outer membrane protein
?NC_000913 380853 = 58 (0.740)pseudogene (408/417 nt) yaiX pseudogene, interrupted by IS2A, hexapeptide transferase superfamily, putative transferase
* ? NC_000913 = 83665184 (1.060)3 (0.040) 3/494 NT 3.4% coding (301/1086 nt) ybiC putative dehydrogenase
?NC_000913 = 836897 89 (1.160)coding (547/1086 nt) ybiC putative dehydrogenase
* ? NC_000913 = 96959774 (0.930)4 (0.050) 3/504 NT 4.7% coding (209/1233 nt) ycaQ DUF1006 family protein with C‑terminal wHTH domain
?NC_000913 = 969716 91 (1.170)coding (328/1233 nt) ycaQ DUF1006 family protein with C‑terminal wHTH domain
* ? NC_000913 1207790 =36 (0.450)41 (0.550) 29/482 NT 57.8% coding (290/630 nt) stfP e14 prophage, uncharacterized protein
?NC_000913 1209619 = 26 (0.350)pseudogene (1/501 nt) stfE pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related
* ? NC_000913 = 120780533 (0.410)52 (0.700) 44/482 NT 64.6% coding (305/630 nt) stfP e14 prophage, uncharacterized protein
?NC_000913 = 1209602 26 (0.350)pseudogene (18/501 nt) stfE pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related
* ? NC_000913 1293032 =0 (0.000)70 (0.880) 51/514 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 = 173197373 (0.920)4 (0.050) 4/494 NT 5.5% coding (2887/4617 nt) lhr putative ATP‑dependent helicase
?NC_000913 = 1732058 66 (0.860)coding (2972/4617 nt) lhr putative ATP‑dependent helicase
* ? NC_000913 1979486 =0 (0.000)36 (0.450) 28/514 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 = 19794890 (0.000)49 (0.620) 37/514 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 2270127 =92 (1.160)8 (0.100) 8/514 NT 8.0% coding (151/567 nt) mepS murein DD‑endopeptidase, space‑maker hydrolase, mutational suppressor of prc thermosensitivity, outer membrane lipoprotein, weak murein LD‑carboxypeptidase
?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 2288917 =NA (NA)3 (0.040) 3/514 NT 5.4% intergenic (‑5/+146) yejO/insH1 pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system/IS5 transposase and trans‑activator
?NC_000913 2876676 = 53 (0.670)coding (98/1038 nt) iap aminopeptidase in alkaline phosphatase isozyme conversion
* ? NC_000913 = 2290111NA (NA)7 (0.090) 7/514 NT 11.9% 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 = 2876679 52 (0.650)coding (101/1038 nt) iap aminopeptidase in alkaline phosphatase isozyme conversion
* ? NC_000913 = 253196362 (0.780)4 (0.050) 3/494 NT 4.9% coding (503/762 nt) cysZ sulfate transporter, sulfite inhibited
?NC_000913 = 2532165 96 (1.260)coding (705/762 nt) cysZ sulfate transporter, sulfite inhibited
* ? NC_000913 2626064 =59 (0.740)3 (0.040) 3/496 NT 4.0% coding (952/1542 nt) ppx exopolyphosphatase
?NC_000913 2626614 = 87 (1.130)coding (1502/1542 nt) ppx exopolyphosphatase
* ? NC_000913 2881788 =67 (0.840)4 (0.050) 4/506 NT 7.4% coding (353/1092 nt) casC CRISP RNA (crRNA) containing Cascade antiviral complex protein
?NC_000913 2882110 = 34 (0.430)coding (31/1092 nt) casC CRISP RNA (crRNA) containing Cascade antiviral complex protein
* ? NC_000913 = 319749481 (1.020)4 (0.050) 3/500 NT 4.9% coding (2146/2841 nt) glnE fused deadenylyltransferase/adenylyltransferase for glutamine synthetase
?NC_000913 = 3197781 76 (0.980)coding (1859/2841 nt) glnE fused deadenylyltransferase/adenylyltransferase for glutamine synthetase
* ? NC_000913 = 3652918NA (NA)3 (0.040) 3/506 NT 6.0% coding (280/1017 nt) insH1 IS5 transposase and trans‑activator
?NC_000913 = 3655092 48 (0.600)coding (411/531 nt) dctR Putative LuxR family repressor for dicarboxylate transport
* ? NC_000913 3837737 =46 (0.580)3 (0.040) 3/506 NT 4.1% coding (786/1185 nt) setC putative arabinose efflux transporter
?NC_000913 3839188 = 95 (1.210)coding (805/819 nt) nlpA cytoplasmic membrane lipoprotein‑28
* ? NC_000913 3857725 =88 (1.110)4 (0.050) 4/496 NT 4.6% coding (679/1494 nt) yidJ sulfatase/phosphatase superfamily protein
?NC_000913 3858257 = 80 (1.040)coding (147/1494 nt) yidJ sulfatase/phosphatase superfamily protein
* ? NC_000913 4295831 =NA (NA)9 (0.130) 4/436 NT NA intergenic (+38/+606) gltP/yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
?NC_000913 = 4296395 NA (NA)noncoding (562/602 nt) RIP321 (repetitive extragenic palindromic) element, contains 11 REP sequences and 4 IHF sites RIP321 (repetitive extragenic palindromic) element, contains 11 REP sequences and 4 IHF sites
* ? NC_000913 4409626 =83 (1.040)3 (0.040) 3/494 NT 4.0% coding (351/732 nt) rlmB 23S rRNA mG2251 2'‑O‑ribose methyltransferase, SAM‑dependent
?NC_000913 4409709 = 66 (0.860)coding (434/732 nt) rlmB 23S rRNA mG2251 2'‑O‑ribose methyltransferase, SAM‑dependent
* ? NC_000913 = 4447213108 (1.360)3 (0.040) 3/494 NT 2.9% coding (3101/3780 nt) tamB translocation and assembly module for autotransporter export, inner membrane subunit
?NC_000913 = 4447555 95 (1.240)coding (3443/3780 nt) tamB translocation and assembly module for autotransporter export, inner membrane subunit
* ? NC_000913 = 455207599 (1.240)4 (0.050) 4/500 NT 4.2% coding (439/1185 nt) uxuA mannonate hydrolase
?NC_000913 = 4552347 86 (1.110)coding (711/1185 nt) uxuA mannonate hydrolase