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
MC JC 257,908 Δ776 bp 100% [crl] [crl]
RA 524,504 T→G 9.4% V415G (GTG→GGG)  rhsD → Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
JC 700,783 Δ9 bp 6.9% coding (804‑812/1221 nt) nagC ← N‑acetylglucosamine‑inducible nag divergent operon transcriptional repressor
JC 1,159,282 +AGT 16.9% coding (1414/1434 nt) ptsG → fused glucose‑specific PTS enzymes: IIB component/IIC component
JC JC 1,159,287 IS2 (–) +5 bp 6.8% coding (1419‑1423/1434 nt) ptsG → fused glucose‑specific PTS enzymes: IIB component/IIC component
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
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 2,132,787 A→C 100% I204S (ATC→AGC)  wcaA ← putative glycosyl transferase
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 2,304,522 G→T 8.7% intergenic (+129/+586) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,304,523 G→C 9.6% intergenic (+130/+585) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,304,537 A→G 9.6% intergenic (+144/+571) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,304,540 C→T 10.1% intergenic (+147/+568) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,304,549 C→T 9.3% intergenic (+156/+559) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,314,716 C→A 8.3% A410E (GCG→GAG)  rcsD → phosphotransfer intermediate protein in two‑component regulatory system with RcsBC
JC 2,521,130 Δ122 bp 5.4% valY valY
RA 3,054,071 A→G 5.4% L257P (CTG→CCG)  pepP ← proline aminopeptidase P II
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]
RA 3,875,533 T→G 8.7% H32Q (CAT→CAG)  yidX → putative lipoprotein
MC JC 3,909,312 Δ774 bp 100% [pstA]–[pstC] [pstA], [pstC]
JC 4,001,645 Δ5 bp 100% coding (220‑224/951 nt) corA → magnesium/nickel/cobalt transporter
RA 4,171,648 A→C 100% noncoding (12/120 nt) rrfB → 5S ribosomal RNA of rrnB operon
RA 4,184,543 C→A 100% P1100Q (CCG→CAG)  rpoB → RNA polymerase, beta subunit
RA 4,296,060 C→T 5.2% intergenic (+266/+376) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,190 A→G 17.2% intergenic (+396/+246) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,191 A→C 20.4% intergenic (+397/+245) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,268 T→C 30.8% intergenic (+474/+168) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,286 C→T 20.7% intergenic (+492/+150) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,303 A→G 7.6% intergenic (+509/+133) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,304 A→C 9.4% intergenic (+510/+132) 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
JC 4,606,166 Δ121 bp 5.4% [leuP] [leuP]

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 1465072 1465376 305 50 [49] [48] 50 ynbG ynbG
* * ÷ NC_000913 3423870–3424449 3424449 1–580 50 [49] [49] 50 [rrlD] [rrlD]
* * ÷ NC_000913 4110659 4111548 890 50 [49] [49] 50 [cdh]–tpiA [cdh],tpiA

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 1207790 =49 (0.410)41 (0.360) 36/488 NT 46.9% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 47 (0.420)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 120780547 (0.390)50 (0.440) 43/488 NT 52.3% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 47 (0.420)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related