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
MC JC 257,908 Δ776 bp [crl] [crl]
JC JC 458,790 IS186 (–) +6 bp :: Δ1 bp intergenic (+90/‑93) clpX → / → lon ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La
RA 1,020,956 A→G intergenic (‑37/‑182) sulA ← / → sxy SOS cell division inhibitor/CRP‑S‑dependent promoter expression factor
RA 1,196,305 C→T R395C (CGT→TGT)  icd → isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase
MC JC 1,411,925 Δ23,060 bp [ttcA]–[ttcC] 33 genes
MC JC 1,978,503 Δ776 bp insB1–insA insB1, insA
JC JC 1,979,486 IS5 (+) +4 bp intergenic (‑271/‑264) insA ← / → uspC IS1 repressor TnpA/universal stress protein
RA 2,132,787 A→C I204S (ATC→AGC)  wcaA ← putative glycosyl transferase
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 3,214,415 A→C I457L (ATT→CTT)  rpoD → RNA polymerase, sigma 70 (sigma D) factor
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]
JC 4,001,645 Δ5 bp coding (220‑224/951 nt) corA → magnesium/nickel/cobalt transporter
RA 4,049,886 T→C intergenic (+134/‑13) polA → / → spf 5' to 3' DNA polymerase and 3' to 5'/5' to 3' exonuclease/Spot 42 sRNA antisense regulator of galK translation, Hfq‑dependent
RA 4,184,543 C→A P1100Q (CCG→CAG)  rpoB → RNA polymerase, beta subunit
RA 4,296,381 +GC intergenic (+587/+55) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 1293040 1309404 16365 40 [0] [0] 50 tdk–[kch] tdk,insZ,insZ,insZ,adhE,ychE,oppA,oppB,oppC,oppD,oppF,yciU,clsA,yciY,[kch]
* * ÷ NC_000913 2066274–2066612 2066612 1–339 20 [18] [18] 19 [insH1] [insH1]
* * ÷ NC_000913 3423739–3424528 3424528 1–790 19 [17] [17] 20 [rrfD]–[rrlD] [rrfD],[rrlD]
* * ÷ NC_000913 4233730 4235425 1696 19 [18] [18] 19 pgi pgi

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 257908 =NA (NA)40 (0.850) 34/284 0.4 100% noncoding (768/768 nt) IS1 repeat region
?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 = 258675NA (NA)50 (1.060) 44/284 0.1 100% noncoding (1/768 nt) IS1 repeat region
?NC_000913 1309405 = 0 (0.000)coding (865/1254 nt) kch voltage‑gated potassium channel
* ? NC_000913 1207790 =4 (0.080)36 (0.860) 30/252 0.4 86.2% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 8 (0.190)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 12078054 (0.080)33 (0.790) 30/252 0.4 85.1% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 8 (0.190)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related