breseq  version 0.39.0  
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation annotation gene description
RA 165,749 Δ1 bp intergenic (+42/‑5) rrnI‑5S → / → trnI‑Asn ribosomal RNA‑5S/tRNA‑Asn
RA 165,751 Δ1 bp intergenic (+44/‑3) rrnI‑5S → / → trnI‑Asn ribosomal RNA‑5S/tRNA‑Asn
RA 165,826 +C intergenic (+1/‑4) trnI‑Asn → / → trnI‑Thr tRNA‑Asn/tRNA‑Thr
RA 166,037 +T intergenic (+4/‑27) trnI‑Gly → / → trnI‑Arg tRNA‑Gly/tRNA‑Arg
RA 166,345 Δ1 bp intergenic (+17/‑155) trnI‑Ala → / → rrnH‑16S tRNA‑Ala/ribosomal RNA‑16S
RA 634,436 A→G intergenic (+574/‑674) gmuG → / → trnE‑Arg exported mannan endo‑1,4‑beta‑mannosidase/tRNA‑Arg
RA 1,317,152 +GT intergenic (+23/+5) phrA → / ← yjpA secreted inhibitor of the activity of phosphatase RapA (quorum sensing)/putative enzyme
RA 1,317,158 (T)5→6 coding (257/258 nt) yjpA ← putative enzyme
RA 2,097,087 (A)7→8 intergenic (‑111/+39) azoJ ← / ← yocK FMN‑dependent NADH‑azoreductase/putative general stress protein
RA 2,271,424 T→C R78R (AGA→AGG)  uvrX ← lesion bypass phage DNA polymerase; phage SPbeta
RA 2,271,505 C→T V51V (GTG→GTA)  uvrX ← lesion bypass phage DNA polymerase; phage SPbeta
RA 2,271,523 A→C D45E (GAT→GAG)  uvrX ← lesion bypass phage DNA polymerase; phage SPbeta
RA 2,480,646 2 bp→AT intergenic (+21/+103) zwf → / ← gndA glucose‑6‑phosphate 1‑dehydrogenase (NADP‑dependent)/NADP+‑dependent 6‑P‑gluconate dehydrogenase
RA 2,480,654 Δ1 bp intergenic (+29/+96) zwf → / ← gndA glucose‑6‑phosphate 1‑dehydrogenase (NADP‑dependent)/NADP+‑dependent 6‑P‑gluconate dehydrogenase
RA 2,480,667 Δ1 bp intergenic (+42/+83) zwf → / ← gndA glucose‑6‑phosphate 1‑dehydrogenase (NADP‑dependent)/NADP+‑dependent 6‑P‑gluconate dehydrogenase
RA 2,581,732 (T)6→7 intergenic (‑115/+39) pstS ← / ← pbpA phosphate ABC transporter (phosphate binding lipoprotein)/transpeptidase (penicillin‑binding protein 2A)
RA 3,770,066 (A)8→9 intergenic (‑613/+38) ywzE ← / ← csbD conserved protein of unknown function (putative phage interference protein)/stress response protein
RA 3,935,825 Δ1 bp coding (1190/1191 nt) rlmI ← large subunit ribosomal RNA m5C1962 methyltransferase
RA 4,155,395 (A)5→6 intergenic (‑186/+38) trnY‑Lys ← / ← purA tRNA‑Lys/adenylosuccinate synthetase

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000964 161197–161239 165468–164903 3665–4272 9 [6] [6] 10 [rrnI‑16S]–[rrnI‑23S] [rrnI‑16S],[rrnI‑23S]
* * ÷ NC_000964 166722–166813 171072–170392 3580–4351 7 [6] [6] 9 [rrnH‑16S]–[rrnH‑23S] [rrnH‑16S],[rrnH‑23S]
* * ÷ NC_000964 171583–171678 176099–172533 856–4517 7 [5] [5] 7 [rrnG‑16S]–[rrnG‑23S] [rrnG‑16S],[rrnG‑23S]
* * ÷ NC_000964 529514 634383 104870 11 [0] [0] 44 [ydcL]–gmuG [ydcL],immA,immR,xis,ydzL,ydcO,BSU_04849,helP,conQ,nicK,ydcS,ydcT,yddA,conB,conC,conD,conE,yddF,conG,cwlT,yddI,yddJ,yddK,rapI,phrI,yddM,yddN,lrpA,lrpB,yddQ,yddR,yddS,ydzM,yddT,ydzN,sufLC,cspC,cdnL,ydzE,ydeC,ydeD,ydeE,ydeF,ydeG,ydeH,ydeI,ydeJ,ydeK,ydeL,ydeM,ydeN,ydzF,ydeO,ydeP,ydeQ,ydeR,ydeS,ydzO,aseR,arsF,ydfB,ydfC,ydfD,ydfE,ydfF,ydfG,ydzP,ydzQ,ydfH,ydfI,ydfJ,cesA,ydfK,ydfL,mneP,ydfN,ydfO,ydfP,ydfQ,ydzH,ydzR,ydfR,ydfS,cotP,ydgA,ydgB,ydgC,ydgD,ydgE,vmlR,ydgF,dinB,ydgG,ydgH,ydgI,ydgJ,ydgK,ydhB,ydhC,spoL,ydhE,ydhF,phoB,fra,ydhH,ydhI,ydhJ,ydhK,pbuE,gmuB,gmuA,gmuC,gmuD,gmuR,gmuE,gmuF,gmuG

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000964 634384 =0 (0.000)40 (0.720)
+36 bp		 38/422 0.5 65.2% intergenic (+522/‑726) gmuG/trnE‑Arg exported mannan endo‑1,4‑beta‑mannosidase/tRNA‑Arg
?NC_000964 3788113 = 50 (0.770)intergenic (‑110/+313) atpI/upp ATP synthase (subunit i)/uracil phosphoribosyltransferase