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 76,805 T→A E165D (GAA→GAT)  sgrR ← DNA‑binding transcriptional dual regulator SgrR
RA 87,481 C→A T42K (ACA→AAA)  ilvH → acetolactate synthase/acetohydroxybutanoate synthase, regulatory subunit
RA 125,085 Δ1 bp coding (2069/2664 nt) aceE → pyruvate dehydrogenase E1 component
MC JC 257,908 Δ776 bp insB9–[crl] insB9, insA9, [crl]
RA 326,176 G→T P358T (CCG→ACG)  betA ← choline dehydrogenase
JC JC 568,268 IS1 (–) +9 bp intergenic (+21/‑39) renD → / → emrE DLP12 prophage; protein RenD/multidrug/betaine/choline efflux transporter EmrE
RA 1,196,220 C→T H366H (CAC→CAT)  icd → isocitrate dehydrogenase
RA 1,196,232 C→T T370T (ACC→ACT)  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 1,978,503 Δ776 bp insB‑5–insA‑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 2,416,622 C→G Q626E (CAG→GAG)  pta → phosphate acetyltransferase
RA 2,662,023 T→C I37V (ATT→GTT)  iscR ← DNA‑binding transcriptional dual regulator IscR
RA 3,041,398 T→G L29R (CTT→CGT)  ygfZ → folate‑binding protein
RA 3,176,209 C→A D209Y (GAT→TAT)  cpdA ← cAMP phosphodiesterase
RA 3,560,455 +G pseudogene (151/758 nt) glpR ← DNA‑binding transcriptional repressor GlpR
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 4,184,543 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 366237 366431 195 16 [15] [15] 16 [lacZ]–[lacI] [lacZ],[lacI]
* * ÷ NC_000913 1196241 1211448 15208 16 [15] [15] 16 [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 3621182–3622309 3653126–3652031 29723–31945 17 [15] [15] 16 [rhsB]–[insH‑11] [rhsB],yhhH,yhhI,yhhJ,rbbA,yhiI,yhiJ,yhiL,yhiM,yhiN,pitA,uspB,uspA,dtpB,rsmJ,prlC,rlmJ,gor,dinQ,agrA,agrB,arsR,arsB,arsC,yhiS,[insH‑11]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 = 12994980 (0.000)49 (1.010) 44/276 0.1 100% intergenic (+253/‑33) ychE/insH21 putative inner membrane protein/IS5 transposase and trans‑activator
?NC_000913 1300698 = 0 (0.000)intergenic (+151/‑484) insH21/oppA IS5 transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein