breseq  version 0.27.1  revision 87c22d663cc3
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]
RA 1,263,642 T→G intergenic (‑142/‑72) lolB ← / → hemA lipoprotein localization factor/glutamyl tRNA reductase
JC JC 1,292,997 IS2 (–) +5 bp intergenic (‑75/‑526) hns ← / → tdk global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
RA 1,381,114 G→C pseudogene (294/957 nt) ycjV → pseudogene; putative ATP‑binding component of a transport system
RA 1,529,175 T→C pseudogene (1274/2037 nt) rhsE → pseudogene, Rhs family
RA 1,529,180 T→C pseudogene (1279/2037 nt) rhsE → pseudogene, Rhs family
RA 1,529,185 C→T pseudogene (1284/2037 nt) rhsE → pseudogene, Rhs family
RA 1,529,203 C→A pseudogene (1302/2037 nt) rhsE → pseudogene, Rhs family
RA 1,529,218 C→T pseudogene (1317/2037 nt) rhsE → pseudogene, Rhs family
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
JC 2,769,750 (GGCTGTCA)2→3 coding (48/702 nt) yfjR → CP4‑57 prophage; putative DNA‑binding transcriptional regulator
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
JC 4,186,115 (TTCCGCTGG)1→2 coding (766/4224 nt) rpoC → RNA polymerase, beta prime 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 1978464 1979282 819 64 [62] [62] 63 insB1–insA insB1, insA
* * ÷ NC_000913 2066337–2067115 2067115 1–779 63 [62] [61] 64 insH1 IS5 transposase and trans‑activator
* * ÷ NC_000913 3423810–3424234 3424527–3424238 5–718 65 [62] [61] 63 [rrlD] [rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 = 19785020 (0.000)52 (0.370) 42/448 2.5 100% intergenic (‑305/+16) flhD/insB1 flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B
?NC_000913 1979279 = 0 (0.000)intergenic (‑64/‑474) insA/uspC IS1 repressor TnpA/universal stress protein