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

Predicted mutations
evidence position mutation freq annotation gene description
RA 373,857 G→A 6.4% intergenic (‑33/+61) frmB ← / ← frmA S‑formylglutathione hydrolase/alcohol dehydrogenase class III/glutathione‑dependent formaldehyde dehydrogenase
RA 449,933 G→A 11.3% M2I (ATG→ATA)  bolA → stationary‑phase morphogene, transcriptional repressor for mreB; also regulator for dacA, dacC, and ampC
RA 479,438 C→A 100% G141V (GGC→GTC)  acrB ← multidrug efflux system protein
JC JC 481,433 IS5 (+) +4 bp 100% coding (217‑220/648 nt) acrR → transcriptional repressor
RA 762,240 C→T 12.4% A267A (GCC→GCT)  mngA → fused 2‑O‑a‑mannosyl‑D‑glycerate specific PTS enzymes: IIA component/IIB component/IIC component
RA 802,634 G→A 10.6% T35I (ACC→ATC)  ybhC ← acyl‑CoA thioesterase, lipoprotein
RA 1,184,046 T→G 100% E396A (GAG→GCG)  phoQ ← sensory histidine kinase in two‑component regulatory system with PhoP
RA 1,529,194 G→A 6.4% intergenic (+68/+28) nhoA → / ← yddE N‑hydroxyarylamine O‑acetyltransferase/PhzC‑PhzF family protein
RA 1,597,224 T→A 12.2% V493D (GTC→GAC)  lsrA → autoinducer 2 import ATP‑binding protein
JC 1,613,357 Δ20 bp 94.9% intergenic (‑192/‑1) marC ← / → marR UPF0056 family inner membrane protein/transcriptional repressor of multiple antibiotic resistance
RA 1,713,241 A→G 8.1% Y207H (TAC→CAC)  anmK ← anhydro‑N‑acetylmuramic acid kinase
JC 2,656,826 +GCGCGCA 100% coding (26/804 nt) suhB → inositol monophosphatase
RA 2,889,135 T→A 9.5% N2Y (AAT→TAT) 
*260C (TGA→TGT) 		 ygcQ ←
ygcR ←		 putative flavoprotein
putative flavoprotein
RA 3,207,739 A→C 100% D445A (GAT→GCT)  rpoD → RNA polymerase, sigma 70 (sigma D) factor
RA 3,665,311 C→T 9.5% intergenic (‑57/‑463) yhjB ← / → yhjC putative DNA‑binding transcriptional response regulator/LysR family putative transcriptional regulator
RA 4,153,506 T→A 8.7% intergenic (‑308/‑61) trmA ← / → btuB tRNA m(5)U54 methyltransferase, SAM‑dependent; tmRNA m(5)U341 methyltransferase/vitamin B12/cobalamin outer membrane transporter

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ CP009273 716339 716482 144 11 [8] [8] 9 ybfK/kdpE uncharacterized protein/response regulator in two‑component regulatory system with KdpD
* * ÷ CP009273 993016 993272 257 9 [8] [7] 9 ssuE/elfA NAD(P)H‑dependent FMN reductase/laminin‑binding fimbrin subunit
* * ÷ CP009273 1059438 1059498 61 10 [8] [7] 16 [yccE] [yccE]
* * ÷ CP009273 1164349 1164448 100 9 [8] [7] 9 ycfQ/bhsA repressor for bhsA(ycfR)/biofilm, cell surface and signaling protein
* * ÷ CP009273 1207527 1207704 178 11 [8] [8] 9 iraM/ycgX RpoS stabilzer during Mg starvation, anti‑RssB factor/DUF1398 family protein
* * ÷ CP009273 1524295 1524652 358 9 [8] [7] 9 ydcD uncharacterized protein
* * ÷ CP009273 1540250 1540505 256 9 [8] [8] 9 [yddL] [yddL]
* * ÷ CP009273 2004662 2004768 107 9 [7] [8] 9 [yedN] [yedN]
* * ÷ CP009273 2027277 2027458 182 9 [8] [6] 9 rseX/yedS sRNA antisense regulator of ompA and ompC translation, Hfq‑dependent/pseudogene, outer membrane protein homology; putative outer membrane protein
* * ÷ CP009273 2449256 2449466 211 9 [8] [8] 9 yfcV/sixA putative fimbrial‑like adhesin protein/phosphohistidine phosphatase
* * ÷ CP009273 2463865 2463931 67 9 [8] [8] 9 gtrS serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
* * ÷ CP009273 2569306 2569358 53 9 [8] [8] 10 eutS/maeB putative ethanol utilization carboxysome structural protein/malic enzyme: putative oxidoreductase/putative phosphotransacetylase
* * ÷ CP009273 3575377 3575541 165 10 [8] [6] 9 yhhZ putative Hcp1 family polymorphic toxin protein; putative colicin‑like DNase/tRNase activity
* * ÷ CP009273 3715543 3715616 74 12 [8] [8] 9 sokA/glyS pseudogene, sRNA antisense regulator blocking mokA/hokA translation/glycine tRNA synthetase, beta subunit
* * ÷ CP009273 3792502 3792739 238 9 [8] [8] 9 [waaU]–[waaZ] [waaU],[waaZ]
* * ÷ CP009273 3798121 3798408 288 9 [7] [8] 9 waaS lipopolysaccharide core biosynthesis protein

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP009273 360104 =38 (0.860)39 (0.880) 28/302 NT 51.7% intergenic (‑38/+557) lacZ/lacI pseudogene, truncated/DNA‑binding transcriptional repressor
?CP009273 = 360286 35 (0.790)intergenic (‑220/+375) lacZ/lacI pseudogene, truncated/DNA‑binding transcriptional repressor
* ? CP009273 603467 =NA (NA)4 (0.090) 4/296 NT 11.6% intergenic (+23/‑54) hokE/insL1 toxic polypeptide, small/IS186 transposase
?CP009273 = 834694 31 (0.700)intergenic (‑31/+11) ybiX/fiu Fe(II)‑dependent oxygenase superfamily protein/catecholate siderophore receptor Fiu
* ? CP009273 1203246 =38 (0.860)8 (0.200) 7/270 NT 21.3% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?CP009273 1205075 = 25 (0.630)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? CP009273 = 120326138 (0.860)13 (0.330) 13/270 NT 30.6% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?CP009273 = 1205058 25 (0.630)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? CP009273 4532499 =4 (0.090)19 (0.460) 17/284 NT 54.5% intergenic (+49/‑433) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
?CP009273 4532813 = 28 (0.680)intergenic (+363/‑119) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
* ? CP009273 = 45325074 (0.090)3 (0.070) 3/284 NT 15.9% intergenic (+57/‑425) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
?CP009273 = 4532803 28 (0.680)intergenic (+353/‑129) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)