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 280,246 T→G A445A (GCT→GCG yagF → CP4‑6 prophage; dehydratase family protein
RA 1,613,656 C→T R94C (CGC→TGC)  marR → transcriptional repressor of multiple antibiotic resistance
JC JC 1,765,315 IS5 (+) +4 bp intergenic (+87/‑10) ydiL → / → ydiM putative HTH domain DNA‑binding protein/MFS superfamily sugar transport 1 family protein
RA 2,802,100 T→C pseudogene (426/1178 nt) ygaY → pseudogene, major facilitator transporter superfamily;putative transport; Not classified; putative transport protein
RA 3,959,963 G→T G63C (GGT→TGT)  rho → transcription termination factor
RA 4,214,915 C→T A387V (GCG→GTG)  metH → homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent
RA 4,493,435 (T)6→7 intergenic (‑187/‑440) insG ← / → yjhB IS4 transposase/putative transporter
JC JC 4,630,235 IS30 (+) +2 bp coding (17‑18/141 nt) yjjY → uncharacterized protein

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ CP009273 946660 949096 2437 222 [218] [221] 227 pflB–[focA] pflB,[focA]
* * ÷ CP009273 1290817 1293670 2854 223 [221] [219] 222 adhE adhE
* * ÷ CP009273 1392945 1437177 44233 222 [220] [213] 222 fnr–ldhA fnr,ogt,abgT,abgB,abgA,abgR,mcaS,smrA,ydaM,ydaN,fnrS,dbpA,ttcA,intR,ydaQ,rcbA,ralR,recT,recE,racC,ydaE,kilR,sieB,ydaF,ydaG,racR,ydaS,ydaT,ydaU,ydaV,ydaW,rzpR,rzoR,trkG,ynaK,ydaY,tmpR,lomR,insH1,lomR,stfR,tfaR,pinR,ynaE,ttcC,uspF,ompN,micC,pfo,ydbJ,hslJ,ldhA
* * ÷ CP009273 2408149 2410427 2279 222 [220] [220] 223 [ackA]–pta [ackA],pta
* * ÷ CP009273 4369115 4370421 1307 224 [220] [218] 227 [frdD]–[frdA] [frdD],frdC,frdB,[frdA]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP009273 360104 =645 (1.570)590 (1.440) 222/296 0.0 47.8% 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 = 1391495NA (NA)394 (0.960) 180/296 0.4 97.5% intergenic (+146/‑127) insH1/ynaJ IS5 transposase and trans‑activator/DUF2534 family putative inner membrane protein
?CP009273 = 1972751 10 (0.020)intergenic (‑297/‑483) flhD/uspC flagellar class II regulon transcriptional activator, with FlhC/universal stress protein
* ? CP009273 1972748 =7 (0.020)382 (0.940) 161/294 1.0 98.2% intergenic (‑294/‑486) flhD/uspC flagellar class II regulon transcriptional activator, with FlhC/universal stress protein
?CP009273 = 2283592 NA (NA)noncoding (1/1195 nt) IS5 repeat region