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 557,870 (T)5→6 intergenic (+421/‑3) yddT → / → ydzN putative exported phage protein/hypothetical protein
RA 608,219 (A)5→6 intergenic (‑144/+27) ydgF ← / ← dinB putative amino acid permease/nuclease inhibitor
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 2,107,958 A→G I267I (ATT→ATC)  odhB ← 2‑oxoglutarate dehydrogenase complex (dihydrolipoamide transsuccinylase, E2 subunit)
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 161189–161234 162857–161243 10–1669 5 [4] [4] 5 [rrnI‑16S]–[rrnI‑23S] [rrnI‑16S],[rrnI‑23S]
* * ÷ NC_000964 166716–166779 171081–170066 3288–4366 5 [4] [3] 6 [rrnH‑16S]–[rrnH‑23S] [rrnH‑16S],[rrnH‑23S]
* * ÷ NC_000964 171577–171679 176104–172533 855–4528 6 [4] [4] 5 [rrnG‑16S]–[rrnG‑23S] [rrnG‑16S],[rrnG‑23S]
* * ÷ NC_000964 1886370 1886544 175 5 [4] [4] 5 [ynaI] [ynaI]
* * ÷ NC_000964 2019367 2107483 88117 5 [3] [4] 6 yoxC–yocS yoxC,yoxB,yoaA,yoaB,yoaC,yoaD,yoaE,yoaF,yoaG,BSU_18595,BSU_18596,yozQ,yoaH,yoaI,exlX,yoaK,pelB,yoaM,yozS,oxdD,yoaO,BSU_18689,yoaP,yoaQ,yozT,yozF,yoaR,yoaS,yozG,yoaT,yoaU,yoaV,yoaW,yoaZ,penP,yobA,yobB,yppS,xynA,yozV,yobD,yozH,yozI,yobE,yobF,yozW,yozX,yozJ,yozY,rapK,phrK,yozL,yozM,yobI,bsrE,yobJ,rttM,rttL,yobM,yobN,yobO,csaA,yobQ,yobR,yobS,yobT,yobU,yobV,yobW,czrA,yocA,yozB,yocB,yocC,yocD,desE,desK,desR,walL,recQ,azoJ,yocK,yocL,yoyB,yocM,yozN,yocN,yozO,yozC,dhaS,sqhC,sodF,yocR,yocS
* * ÷ NC_000964 2214697 2214795 99 5 [4] [4] 5 yopC conserved protein of unknown function; phage SPbeta
* * ÷ NC_000964 4173938 4174024 87 5 [3] [3] 5 yybM putative transporter permease subunit

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000964 = 64753718 (0.360)27 (0.550) 27/464 0.7 59.7% coding (447/648 nt) rex transcription repressor of cydABCD and yjlC‑ndh expression
?NC_000964 647562 = 19 (0.390)coding (472/648 nt) rex transcription repressor of cydABCD and yjlC‑ndh expression