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

Predicted mutations
evidence seq id position mutation annotation gene description
JC CP009273 103,910 (CTTCCAGGAC)1→2 coding (867/918 nt) lpxC → UDP‑3‑O‑acyl N‑acetylglucosamine deacetylase
RA CP009273 155,132 C→G R161P (CGC→CCC)  pcnB ← poly(A) polymerase
MC JC CP009273 354,080 Δ9 bp coding (314‑322/900 nt) cynR ← transcriptional activator of cyn operon; autorepressor
RA CP009273 407,471 C→T W156* (TGG→TAG)  araJ ← arabinose‑inducible putative transporter, MFS family
RA CP009273 829,599 G→T M358I (ATG→ATT)  dinG → ATP‑dependent DNA helicase
MC JC CP009273 2,400,028 Δ9 bp coding (85‑93/939 nt) lrhA ← transcriptional repressor of flagellar, motility and chemotaxis genes
RA CP009273 2,681,289 C→A D292Y (GAT→TAT)  glrR ← response regulator regulating glmY sRNA in two‑component system with sensor protein GlrK
RA CP009273 2,901,251 C→A G17V (GGT→GTT)  eno ← enolase
RA CP009273 3,208,093 T→C F563S (TTC→TCC)  rpoD → RNA polymerase, sigma 70 (sigma D) factor
RA CP009273 3,433,439 C→A R317L (CGC→CTC)  rpoA ← RNA polymerase, alpha subunit
RA CP009273 3,466,500 G→A T125I (ACC→ATC)  fusA ← protein chain elongation factor EF‑G, GTP‑binding
RA CP009273 3,547,518 G→A E359K (GAA→AAA)  malT → mal regulon transcriptional activator
RA CP009273 3,729,347 G→A E337K (GAG→AAG)  xylR → xylose divergent operon transcriptional activator
RA CP009273 4,173,770 T→G D866E (GAT→GAG)  rpoB → RNA polymerase, beta subunit
RA CP009273 4,275,144 C→T intergenic (‑3/+197) yjcH ← / ← acs DUF485 family inner membrane protein/acetyl‑CoA synthetase
RA CP009273 4,276,215 C→A R362L (CGC→CTC)  acs ← acetyl‑CoA synthetase
RA CP009273 4,629,517 C→T V203M (GTG→ATG)  arcA ← response regulator in two‑component regulatory system with ArcB or CpxA

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ CP009273 1800621 1801543 923 16 [14] [15] 17 [pfkB] [pfkB]
* * ÷ CP009273 1929098 1930575 1478 16 [15] [12] 16 [zwf] [zwf]
* * ÷ CP009273 4097478 4098434 957 17 [14] [14] 17 [pfkA] [pfkA]
* * ÷ CP009273 4209763 4232203 22441 67 [3] [0] 54 [aceK]–xylE [aceK],arpA,iclR,metH,yjbB,pepE,rluF,yjbD,lysC,pgi,yjbE,yjbF,yjbG,yjbH,yjbT,psiE,xylE

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP009273 = 270860NA (NA)71 (1.290) 31/134 0.2 85.5% noncoding (320/1221 nt) IS30 repeat region
?CP009273 = 1104830 12 (0.220)coding (40/1536 nt) opgG osmoregulated periplasmic glucan (OPG) biosynthesis periplasmic protein
* ? CP009273 360104 =47 (0.850)99 (1.790) 40/134 0.0 67.8% intergenic (‑38/+557) lacZ/lacI pseudogene, truncated/DNA‑binding transcriptional repressor
?CP009273 = 360286 NA (NA)intergenic (‑220/+375) lacZ/lacI pseudogene, truncated/DNA‑binding transcriptional repressor
* ? CP009273 1104827 =8 (0.140)70 (1.270) 33/134 0.1 89.7% coding (37/1536 nt) opgG osmoregulated periplasmic glucan (OPG) biosynthesis periplasmic protein
?CP009273 = 1391495 NA (NA)intergenic (+146/‑127) insH1/ynaJ IS5 transposase and trans‑activator/DUF2534 family putative inner membrane protein
* ? CP009273 1551066 =51 (0.920)148 (2.680) 48/134 0.0 73.5% coding (185/432 nt) osmC lipoyl‑dependent Cys‑based peroxidase, hydroperoxide resistance; salt‑shock inducible membrane protein; peroxiredoxin
?CP009273 = 1558208 56 (1.010)coding (1783/2400 nt) dosP oxygen sensor, c‑di‑GMP phosphodiesterase, heme‑regulated; cold‑ and stationary phase‑induced bioflim regulator
* ? CP009273 3576788 =NA (NA)64 (1.160) 35/134 0.1 95.5% intergenic (+10/‑55) yrhA/insA pseudogene, interrupted by IS1E/IS1 repressor TnpA
?CP009273 = 4209762 3 (0.050)coding (1239/1737 nt) aceK isocitrate dehydrogenase kinase/phosphatase
* ? CP009273 = 3577555NA (NA)54 (0.980) 32/134 0.2 100% intergenic (+15/‑1) insB1/yrhA IS1 transposase B/pseudogene, interrupted by IS1E
?CP009273 4232204 = 0 (0.000)intergenic (‑22/+350) xylE/malG D‑xylose transporter/maltose transporter subunit
* ? CP009273 4532499 =9 (0.160)61 (1.280) 33/116 0.1 89.2% intergenic (+49/‑433) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
?CP009273 4532813 = 7 (0.150)intergenic (+363/‑119) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
* ? CP009273 = 45325079 (0.160)49 (1.020) 22/116 0.5 86.9% intergenic (+57/‑425) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
?CP009273 = 4532803 7 (0.150)intergenic (+353/‑129) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
* ? Exported 1 =0 (0.000)11547 (1.200) 122/134 0.2 100% coding (792/792 nt) aadA aminoglycoside adenylyltransferase (Murphy, 1985)
?Exported = 3344 NA (NA)intergenic (+1110/–) fdh/– formate dehydrogenase from Pseudomonas sp. 101 with an N‑terminal his‑tag/–
* ? Exported = 900NA (NA)10732 (1.110) 123/134 0.2 97.6% intergenic (‑108/‑111) aadA/fdh aminoglycoside adenylyltransferase (Murphy, 1985)/formate dehydrogenase from Pseudomonas sp. 101 with an N‑terminal his‑tag
?Exported 906 = 266 (0.030)intergenic (‑114/‑105) aadA/fdh aminoglycoside adenylyltransferase (Murphy, 1985)/formate dehydrogenase from Pseudomonas sp. 101 with an N‑terminal his‑tag