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]
MC JC 755,308 Δ102 bp coding (132‑233/390 nt) sdhC → succinate dehydrogenase, membrane subunit, binds cytochrome b556
JC JC 1,293,032 IS1 (–) +8 bp intergenic (‑110/‑488) hns ← / → tdk global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
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 2,862,760 C→T R142R (CGC→CGT)  ygbK → FliA‑regulated DUF1537 family protein
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 4,184,543 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 761513 762742 1230 6 [5] [5] 7 sucB sucB
* * ÷ NC_000913 2066269–2066464 2066577–2066468 5–309 6 [5] [3] 6 [insH1] [insH1]
* * ÷ NC_000913 3423787–3424234 3424515–3424239 6–729 6 [5] [5] 7 [rrfD]–[rrlD] [rrfD],[rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 = 227444NA (NA)8 (0.230) 7/230 2.7 NA noncoding (1686/2904 nt) rrlH 23S ribosomal RNA of rrnH operon
?NC_000913 = 227459 NA (NA)noncoding (1701/2904 nt) rrlH 23S ribosomal RNA of rrnH operon
* ? NC_000913 = 120780516 (0.440)6 (0.190) 6/208 2.7 23.6% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 25 (0.790)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 12994980 (0.000)34 (0.970) 33/232 0.2 98.6% intergenic (+253/‑1684) ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
?NC_000913 1300698 = 1 (0.030)intergenic (+1453/‑484) ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
* ? NC_000913 = 3943635NA (NA)7 (0.200) 7/226 2.6 33.1% intergenic (+125/‑69) gltU/rrlC tRNA‑Glu/23S ribosomal RNA of rrnC operon
?NC_000913 = 4037446 15 (0.410)intergenic (+111/‑73) alaT/rrlA tRNA‑Ala/23S ribosomal RNA of rrnA operon
* ? NC_000913 = 417180351 (1.400)18 (0.500) 13/236 1.6 26.6% intergenic (+47/‑254) rrfB/murB 5S ribosomal RNA of rrnB operon/UDP‑N‑acetylenolpyruvoylglucosamine reductase, FAD‑binding
?NC_000913 = 4213162 49 (1.370)intergenic (+3/‑72) rrfE/yjaA 5S ribosomal RNA of rrnE operon/stress‑induced protein