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

Predicted mutations
evidence position mutation annotation gene description
MC JC 257,908 Δ776 bp insB9[crl] insB9, insA9, [crl]
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 803,662 C→A L54I (CTT→ATT)  ybhJ → putative hydratase YbhJ
MC JC 1,042,956 Δ72,555 bp [etk]mdtG 71 genes
MC JC 1,299,499 Δ1,199 bp insH21 insH21
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 2,196,426 Δ46,519 bp yehF[yeiB] 37 genes
RA 2,242,968 G→T intergenic (‑1/+16) yeiB ← / ← folE DUF418 domain‑containing protein YeiB/GTP cyclohydrolase 1
RA 2,243,185 C→T T156T (ACG→ACA folE ← GTP cyclohydrolase 1
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 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 3,436,697 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 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 4,278,657 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 3423876–3424234 3424412–3424238 5–537 9 [8] [8] 9 [rrlD] [rrlD]
* * ÷ NC_000913 3619008 3718319 99312 18 [0] [8] 9 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 =25 (0.290)36 (0.450) 36/456 0.7 67.1% coding (290/630 nt) ycfK protein StfP
?NC_000913 1209619 = 12 (0.150)intergenic (‑500/‑66) tfaE/pinE putative tail fiber assembly protein TfaE/site‑specific DNA recombinase
* ? NC_000913 = 120780522 (0.260)53 (0.660) 47/456 0.4 76.5% coding (305/630 nt) ycfK protein StfP
?NC_000913 = 1209602 12 (0.150)intergenic (‑483/‑83) tfaE/pinE putative tail fiber assembly protein TfaE/site‑specific DNA recombinase