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 83,579 (A)7→8 intergenic (‑50/+43) leuA ← / ← leuL 2‑isopropylmalate synthase/leu operon leader peptide
RA 124,078 C→T D354D (GAC→GAT aceE → pyruvate dehydrogenase E1 component
MC JC 257,908 Δ776 bp insB9[crl] insB9, insA9, [crl]
RA 403,205 (T)7→8 intergenic (+43/‑76) phoA → / → psiF alkaline phosphatase/phosphate starvation‑inducible protein PsiF
RA 421,256 A→G T91A (ACC→GCC)  proY → putative transporter ProY
RA 498,116 C→T P21L (CCT→CTT)  hemH → ferrochelatase
RA 498,809 A→G K252R (AAA→AGA)  hemH → ferrochelatase
RA 499,060 T→G D305A (GAC→GCC)  aes ← acetylesterase
MC JC 499,082 Δ52,248 bp [aes][ybcF] 46 genes
RA 694,721 C→T G79S (GGC→AGC)  miaB ← isopentenyl‑adenosine A37 tRNA methylthiolase
RA 709,364 A→G D344G (GAT→GGT)  chiP → chitooligosaccharide outer membrane channel
RA 723,528 (T)8→7 coding (887/2685 nt) kdpD ← sensor histidine kinase KdpD
RA 803,662 C→A L54I (CTT→ATT)  ybhJ → putative hydratase YbhJ
RA 851,631 A→G Y323H (TAC→CAC)  opgE ← phosphoethanolamine transferase OpgE
RA 885,118 A→G V38A (GTT→GCT)  ybjH ← uncharacterized protein YbjH
MC JC 1,042,956 Δ72,555 bp [etk]mdtG 71 genes
RA 1,350,723 T→C N106S (AAC→AGC)  fabI ← enoyl‑[acyl‑carrier‑protein] reductase
MC JC 1,351,171 Δ239,229 bp ycjDydeT 230 genes
RA 1,590,430 T→C intergenic (‑429/+424) ydeT ← / ← hipA fimbrial usher domain‑containing protein YdeT/serine/threonine‑protein kinase toxin HipA
RA 1,905,761 G→A G25D (GGT→GAT)  mntP → Mn(2(+)) exporter
MC JC 1,978,503 Δ776 bp insB5insA5 insB5, insA5
MC JC 2,085,042 Δ109,115 bp [tsuA][mrp] 106 genes
MC JC 2,286,372 Δ22,969 bp yejO[alkB] 24 genes
RA 2,311,650 A→G F367S (TTC→TCC)  ompC ← outer membrane porin C
MC JC 2,312,100 24707 bp→A [ompC][gyrA] 16 genes
MC JC 2,348,550 Δ41,411 bp [yfaE][yfbP] 40 genes
RA 2,389,974 T→G intergenic (+10/+74) yfbP → / ← nuoN uncharacterized protein YfbP/NADH:quinone oxidoreductase subunit N
RA 2,390,295 T→G Q404P (CAG→CCG)  nuoN ← NADH:quinone oxidoreductase subunit N
RA 2,424,640 T→C Q198Q (CAA→CAG hisM ← lysine/arginine/ornithine ABC transporter/histidine ABC transporter, membrane subunit HisM
RA 2,531,483 T→A S7S (TCT→TCA cysZ → sulfate:H(+) symporter
RA 2,756,045 T→C intergenic (+90/‑114) ssrA → / → intA tmRNA/integrase IntA
RA 2,756,047 T→C intergenic (+92/‑112) ssrA → / → intA tmRNA/integrase IntA
MC JC 2,756,415 Δ57,799 bp [intA]emrB 53 genes
RA 2,823,802 A→G intergenic (‑33/+47) recA ← / ← pncC DNA recombination/repair protein RecA/NMN aminohydrolase
MC JC 2,823,891 Δ42,638 bp [pncC]ygbN 41 genes
RA 2,925,117 G→A P55L (CCG→CTG)  syd ← SecY‑interacting protein
RA 3,194,362 (G)6→7 coding (1499/1662 nt) yqiK → flotillin family inner membrane protein YqiK
RA 3,214,325 T→C F427L (TTC→CTC)  rpoD → RNA polymerase sigma factor RpoD
RA 3,216,473 A→G Y7H (TAC→CAC)  nfeF ← NADPH‑dependent ferric‑chelate reductase
MC JC 3,216,779 53253 bp→GTC [nfeR]yhaC 50 genes
RA 3,297,193 G→A L316L (CTG→TTG)  yraQ ← permease family protein YraQ
RA 3,321,967 A→G intergenic (‑354/+105) yhbX ← / ← leuU putative hydrolase YhbX/tRNA‑Leu
RA 3,436,697 G→A E60E (GAG→GAA trkA → NAD‑binding component of Trk potassium transporters
RA 3,449,779 G→A S35S (AGC→AGT rpsC ← 30S ribosomal subunit protein S3
RA 3,468,768 C→T W362* (TGG→TGA chiA ← endochitinase
RA 3,474,425 T→C K43R (AAA→AGA)  rpsL ← 30S ribosomal subunit protein S12
RA 3,523,800 C→G Y310* (TAC→TAG mrcA → peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcA
RA 3,560,455 +G intergenic (+589/+167) rtcR → / ← glpG DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG
RA 3,718,336 A→C *237E (TAA→GAA)  yiaF ← DUF3053 domain‑containing protein YiaF
RA 3,725,393 G→A intergenic (‑75/+20) glyQ ← / ← ysaB glycine‑‑tRNA ligase subunit alpha/putative lipoprotein YsaB
RA 3,725,582 C→A C44F (TGC→TTC)  ysaB ← putative lipoprotein YsaB
MC JC 3,725,590 46159 bp→ATCG [ysaB]yibI 41 genes
RA 3,854,281 A→G L120L (TTA→TTG emrD → multidrug efflux pump EmrD
RA 3,922,994 T→C intergenic (‑554/+63) atpI ← / ← rsmG ATP synthase accessory factor AtpI/16S rRNA m(7)G527 methyltransferase
RA 3,939,662 C→T M317I (ATG→ATA hsrA ← putative transporter HsrA
RA 4,101,858 (T)7→8 coding (169/984 nt) kdgT → 2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter
RA 4,106,199 A→G E127G (GAG→GGG)  cpxP → periplasmic protein CpxP
RA 4,123,930 A→T V176E (GTA→GAA)  cytR ← DNA‑binding transcriptional repressor CytR
RA 4,174,041 A→T E320D (GAA→GAT birA → DNA‑binding transcriptional repressor/biotin‑[acetyl‑CoA‑carboxylase] ligase BirA
RA 4,204,890 C→T G348S (GGT→AGT)  purD ← phosphoribosylamine‑‑glycine ligase
RA 4,241,235 A→G G340G (GGT→GGC xylE ← D‑xylose:H(+) symporter
RA 4,278,657 T→C V60A (GTT→GCT)  ghxP → guanine/hypoxanthine transporter GhxP
RA 4,278,682 C→T A68A (GCC→GCT ghxP → guanine/hypoxanthine transporter GhxP
RA 4,279,023 T→C F182S (TTC→TCC)  ghxP → guanine/hypoxanthine transporter GhxP
RA 4,279,034 Δ2 bp coding (556‑557/1350 nt) ghxP → guanine/hypoxanthine transporter GhxP
MC JC 4,279,050 Δ82,373 bp [ghxP][cadC] 72 genes
RA 4,362,045 T→C intergenic (‑111/+506) cadC ← / ← pheU DNA‑binding transcriptional activator CadC/tRNA‑Phe
MC JC 4,488,473 Δ111,735 bp yjgRyjjA 100 genes
RA 4,600,215 +C intergenic (‑26/+23) yjjA ← / ← dnaC DUF2501 domain‑containing protein YjjA/DNA replication protein DnaC

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 1591225 1652794 61570 14 [13] [12] 14 [hipA]–[ynfP] [hipA],hipB,lsrK,lsrR,lsrA,lsrC,lsrD,lsrB,lsrF,lsrG,tam,yneE,uxaB,dgcF,yneG,glsB,sad,yneJ,yneK,ydeA,marC,marR,marA,marB,eamA,ydeE,mgtS,mgtT,mgrR,dgcZ,ydeI,ydeJ,dcp,ydfG,rspR,ydfZ,ydfI,ydfJ,ynfT,ydfK,pinQ,tfaQ,stfQ,nohA,ynfO,ydfO,gnsB,ynfN,ynfR,ynfQ,cspI,rzpQ,rzoQ,rrrQ,ydfR,essQ,ynfU,cspB,cspF,ynfS,ydfT,ydfU,rem,hokD,relE,relB,ydfV,flxA,ydfW,ydfX,dicC,dicA,ydfA,ydfB,ydfC,dicF,dicB,ydfD,[ynfP]
* * ÷ NC_000913 3423887–3424234 3424424–3424238 5–538 14 [13] [13] 15 rrlD 23S ribosomal RNA
* * ÷ NC_000913 3619008 3718313 99306 30 [0] [0] 20 rhsB–ghrB rhsB,yhhH,yhhI,yhhJ,rbbA,yhiI,yhiY,yhiJ,yhiM,yhiN,pitA,uspB,uspA,yriA,yriB,dtpB,rsmJ,prlC,rlmJ,gor,dinQ,agrA,agrB,arsR,arsB,arsC,yhiS,insH11,yhiS,slp,dctR,yhiD,hdeB,hdeA,hdeD,arrS,gadE,gadF,mdtE,mdtF,gadW,gadY,gadX,gadA,ccp,treF,yhjB,rcdB,yhjD,yhjE,yhjG,pdeH,kdgK,yhjJ,dctA,pdeK,bcsC,bcsZ,bcsB,bcsA,yhjR,bcsE,bcsF,bcsG,ldrD,rdlD,yhjV,dppF,dppD,dppC,dppB,dppA,proK,eptB,yhjX,yhjY,tag,yiaC,bisC,yiaD,ghrB

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 1207790 =46 (0.410)32 (0.300) 31/450 1.3 50.4% coding (290/630 nt) ycfK protein StfP
?NC_000913 1209619 = 20 (0.190)intergenic (‑500/‑66) tfaE/pinE putative tail fiber assembly protein TfaE/site‑specific DNA recombinase
* ? NC_000913 = 120780542 (0.370)64 (0.610) 60/450 0.4 68.4% coding (305/630 nt) ycfK protein StfP
?NC_000913 = 1209602 20 (0.190)intergenic (‑483/‑83) tfaE/pinE putative tail fiber assembly protein TfaE/site‑specific DNA recombinase
* ? NC_000913 = 12994980 (0.000)44 (0.400) 39/474 1.0 100% intergenic (+253/‑69) ychE/insH21 MarC family putative inner membrane protein YchE/IS5 family transposase and trans‑activator
?NC_000913 1300698 = 0 (0.000)intergenic (+151/‑484) insH21/oppA IS5 family transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein