breseq  version 0.35.4  revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation annotation gene description
RA 125,387 C→T Q791* (CAG→TAG)  aceE → pyruvate dehydrogenase E1 component
MC JC 257,908 Δ776 bp insB9[crl] insB9, insA9, [crl]
RA 696,470 C→T noncoding (35/75 nt) glnX ← tRNA‑Gln
RA 759,250 G→T R182L (CGC→CTC)  sucA → subunit of E1(0) component of 2‑oxoglutarate dehydrogenase
RA 1,196,220 C→T H366H (CAC→CAT icd → isocitrate dehydrogenase
RA 1,196,232 C→T T370T (ACC→ACT icd → isocitrate dehydrogenase
RA 1,196,245 T→C L375M (TTA→CTG)  icd → isocitrate dehydrogenase
RA 1,196,247 A→G L375M (TTA→CTG icd → isocitrate dehydrogenase
JC JC 1,293,032 IS1 (–) +8 bp intergenic (‑110/‑488) hns ← / → tdk DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase
MC JC 1,299,499 Δ1,199 bp insH21 insH21
MC JC 1,978,503 Δ776 bp insB‑5insA‑5 insB‑5, insA‑5
JC JC 1,979,486 IS5 (+) +4 bp intergenic (‑271/‑264) insA‑5 ← / → uspC IS1 protein InsA/universal stress protein C
RA 2,132,787 A→C I204S (ATC→AGC)  wcaA ← putative colanic acid biosynthesis glycosyl transferase
RA 2,173,363 Δ2 bp pseudogene (915‑916/1358 nt) gatC ← galactitol‑specific PTS enzyme IIC component
RA 2,661,969 C→G V55L (GTT→CTT)  iscR ← DNA‑binding transcriptional dual regulator IscR
RA 3,041,632 T→A V107E (GTG→GAG)  ygfZ → folate‑binding protein
RA 3,351,798 C→T A410T (GCC→ACC)  arcB ← sensory histidine kinase ArcB
RA 3,560,455 +G pseudogene (151/758 nt) glpR ← DNA‑binding transcriptional repressor GlpR
RA 3,637,646 +T coding (5/1500 nt) pitA → metal phosphate:H(+) symporter PitA
MC JC 3,815,859 Δ82 bp [rph] [rph]
JC 4,001,645 Δ5 bp coding (220‑224/951 nt) corA → Ni(2(+))/Co(2(+))/Mg(2(+)) transporter
RA 4,125,097 C→T E572K (GAG→AAG)  priA ← primosome factor N'
RA 4,184,543 C→A P1100Q (CCG→CAG)  rpoB → RNA polymerase subunit beta
RA 4,296,381 +GC intergenic (+587/+55) gltP → / ← yjcO glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 1196268 1211430 15163 14 [13] [12] 14 [icd]–[icdC] [icd],ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,oweE,ymfN,aaaE,ymfR,beeE,jayE,ymfQ,ycfK,tfaP,tfaE,stfE,pinE,mcrA,[icdC]
* * ÷ NC_000913 3423762–3424533 3424533 1–772 14 [13] [12] 14 [rrfD]–[rrlD] [rrfD],[rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 315642 =NA (NA)19 (0.480) 12/270 2.2 NA noncoding (414/1255 nt) IS3 repeat region
?NC_000913 315671 = NA (NA)noncoding (443/1255 nt) IS3 repeat region
* ? NC_000913 315649 =NA (NA)13 (0.320) 11/274 2.5 NA noncoding (421/1255 nt) IS3 repeat region
?NC_000913 315668 = NA (NA)noncoding (440/1255 nt) IS3 repeat region
* ? NC_000913 = 315852NA (NA)39 (0.980) 17/272 1.3 NA noncoding (624/1255 nt) IS3 repeat region
?NC_000913 = 315875 NA (NA)noncoding (647/1255 nt) IS3 repeat region
* ? NC_000913 = 316201NA (NA)14 (0.360) 9/262 2.9 NA noncoding (973/1255 nt) IS3 repeat region
?NC_000913 = 316220 NA (NA)noncoding (992/1255 nt) IS3 repeat region
* ? NC_000913 566777 =NA (NA)3184 (77.940) 277/278 0.0 99.2% noncoding (1/1258 nt) IS3 repeat region
?NC_000913 = 572471 25 (0.610)coding (6/456 nt) ybcN DLP12 prophage; DNA base‑flipping protein
* ? NC_000913 = 56684119 (0.460)14 (0.450)
+34 bp
9/212 2.1 45.7% noncoding (65/1258 nt) IS3 repeat region
?NC_000913 = 572471 25 (0.610)coding (6/456 nt) ybcN DLP12 prophage; DNA base‑flipping protein