breseq  version 0.35.4  revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence seq id position mutation annotation gene description
RA CP009273 132,999 A→G intergenic (‑48/+58) speE ← / ← yacC spermidine synthase (putrescine aminopropyltransferase)/PulS_OutS family protein
RA CP009273 164,770 +G coding (800/2244 nt) fhuA → ferrichrome outer membrane transporter
RA CP009273 375,477 (G)10→8 intergenic (‑140/+47) frmR ← / ← yaiO regulator protein that represses frmRAB operon/outer membrane protein
RA CP009273 760,326 Δ1 bp coding (691/870 nt) sucD → succinyl‑CoA synthetase, NAD(P)‑binding, alpha subunit
RA CP009273 950,711 A→G Y460H (TAC→CAC)  ycaO ← ribosomal protein S12 methylthiotransferase accessory factor
RA CP009273 971,206 T→C N43N (AAT→AAC)  mukE → chromosome condensin MukBEF, MukE localization factor
RA CP009273 1,107,147 Δ1 bp coding (829/2544 nt) opgH → membrane glycosyltransferase; nutrient‑dependent cell size regulator, FtsZ assembly antagonist
RA CP009273 1,256,655 C→A G226V (GGC→GTC)  prs ← phosphoribosylpyrophosphate synthase
RA CP009273 1,390,409 G→C S26T (AGT→ACT)  insH1 → IS5 transposase and trans‑activator
RA CP009273 1,740,594 T→C intergenic (‑210/‑98) ydhQ ← / → valV autotransporter adhesin‑related protein/tRNA‑Val
RA CP009273 1,782,213 C→T A171V (GCA→GTA)  ppsR → bifunctional regulatory protein: PEP synthase kinase and PEP synthase pyrophosphorylase
RA CP009273 1,848,356 C→T W252* (TGG→TGA)  ydjF ← putative DNA‑binding transcriptional regulator
RA CP009273 2,146,001 C→T T203T (ACG→ACA)  yegL ← VMA domain protein
MC JC CP009273 2,400,028 Δ9 bp coding (85‑93/939 nt) lrhA ← transcriptional repressor of flagellar, motility and chemotaxis genes
RA CP009273 2,528,814 G→A D464N (GAC→AAC)  ptsI → PEP‑protein phosphotransferase of PTS system (enzyme I)
RA CP009273 2,659,085 T→C C98R (TGT→CGT)  csiE → stationary phase inducible protein
JC CP009273 3,479,544 +CAT coding (66/633 nt) crp → cAMP‑activated global transcription factor, mediator of catabolite repression
RA CP009273 3,537,666 G→T L180M (CTG→ATG)  bioH ← pimeloyl‑ACP methyl ester carboxylesterase
RA CP009273 3,553,520 C→T G149D (GGC→GAC)  glpR ← GlpR DNA‑binding transcriptional repressor
RA CP009273 3,908,203 C→T A120T (GCT→ACT)  glmU ← fused N‑acetyl glucosamine‑1‑phosphate uridyltransferase/glucosamine‑1‑phosphate acetyl transferase
RA CP009273 3,914,079 G→A A57V (GCA→GTA)  atpF ← F0 sector of membrane‑bound ATP synthase, subunit b
RA CP009273 3,926,222 C→T P516L (CCA→CTA)  kup → potassium transporter
RA CP009273 4,013,966 C→T I127I (ATC→ATT)  ubiB → regulator of octaprenylphenol hydroxylation, ubiquinone synthesis; regulator of 2'‑N‑acetyltransferase; putative ABC1 family protein kinase
RA CP009273 4,021,106 G→A H343Y (CAT→TAT)  fadA ← 3‑ketoacyl‑CoA thiolase (thiolase I)
RA CP009273 4,022,897 C→T A479T (GCC→ACC)  fadB ← fused 3‑hydroxybutyryl‑CoA epimerase/delta(3)‑cis‑delta(2)‑trans‑enoyl‑CoA isomerase/enoyl‑CoA hydratase/3‑hydroxyacyl‑CoA dehydrogenase
RA CP009273 4,087,148 G→A pseudogene (203/543 nt) rhaD ← pseudogene, truncated, rhamnulose‑phosphate aldolase
RA CP009273 4,151,176 T→G V42G (GTC→GGC)  fabR → transcriptional repressor of fabA and fabB
RA CP009273 4,154,051 G→C G162A (GGA→GCA)  btuB → vitamin B12/cobalamin outer membrane transporter
RA CP009273 4,438,792 G→A R95H (CGT→CAT)  chpB → toxin of the ChpB‑ChpS toxin‑antitoxin system
RA CP009273 4,588,157 G→A Q368* (CAG→TAG)  opgB ← phosphoglycerol transferases I and II
RA CP009273 4,597,341 (C)5→4 coding (177/1032 nt) rsmC ← 16S rRNA m(2)G1207 methyltransferase, SAM‑dependent

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ CP009273 782239 783122 884 105 [104] [104] 107 gpmA gpmA
* * ÷ CP009273 1800568 1801595 1028 106 [102] [103] 105 pfkB pfkB
* * ÷ CP009273 1929055 1930626 1572 105 [103] [101] 105 zwf zwf
* * ÷ CP009273 2850401 2853046 2646 105 [102] [101] 107 mutS mutS
* * ÷ CP009273 3778566 3780200 1635 105 [103] [104] 105 gpmM–[envC] gpmM,[envC]
* * ÷ CP009273 3935448–3936755 3937287–3936795 41–1840 106 [103] [104] 105 [rrsC]–[rrlC] [rrsC],gltU,[rrlC]
* * ÷ CP009273 4097412 4098476 1065 106 [103] [103] 105 pfkA pfkA
* * ÷ CP009273 4197972–4199662 4203043–4199702 41–5072 108 [104] [104] 105 rrsE–[rrfE] rrsE,gltV,rrlE,[rrfE]
* * ÷ CP009273 4205372 4210291 4920 106 [103] [104] 106 aceB–[arpA] aceB,aceA,aceK,[arpA]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP009273 1203246 =4 (0.020)137 (0.870) 102/218 0.5 97.3% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?CP009273 1205075 = 4 (0.030)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? CP009273 = 12032614 (0.020)163 (1.040) 109/218 0.3 97.8% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?CP009273 = 1205058 4 (0.030)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? CP009273 4532499 =32 (0.180)142 (0.850) 103/232 0.7 78.5% intergenic (+49/‑433) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
?CP009273 4532813 = 48 (0.290)intergenic (+363/‑119) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
* ? CP009273 = 453250732 (0.180)142 (0.850) 104/232 0.7 78.5% intergenic (+57/‑425) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
?CP009273 = 4532803 48 (0.290)intergenic (+353/‑129) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)