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 1,088,068 A→G I597T (ATC→ACC)  pgaB ← poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine (PGA) N‑deacetylase outer membrane export lipoprotein
RA 1,196,305 C→T R395C (CGT→TGT)  icd → isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase
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 1,299,499 Δ1,199 bp intergenic (+254/‑485) ychE → / → oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
MC JC 1,619,080 Δ35 bp intergenic (‑172/‑6) marC ← / → marR UPF0056 family inner membrane protein/transcriptional repressor of multiple antibiotic resistance
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
MC JC 2,413,513 Δ10 bp coding (44‑53/1203 nt) ackA → acetate kinase A and propionate kinase 2
RA 3,194,572 (T)6→5 intergenic (+47/+151) yqiK → / ← sibD PHB family membrane protein, function unknown/sRNA antisense regulator of toxic IbsD 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]
MC JC 4,001,645 Δ5 bp coding (220‑224/951 nt) corA → magnesium/nickel/cobalt transporter
MC JC 4,049,991 Δ12 bp noncoding (93‑104/109 nt) spf → 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 3423704–3424536 3424536 1–833 32 [31] [31] 33 [rrfD]–[rrlD] [rrfD],[rrlD]
* * ÷ NC_000913 4233747 4235448 1702 32 [29] [31] 32 pgi pgi

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 1207790 =30 (0.430)44 (0.720) 42/252 0.4 66.4% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 18 (0.290)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 120780532 (0.460)35 (0.570) 32/252 1.2 60.2% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 18 (0.290)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related