breseq  version 0.32.0  revision 6ff6de7d1b87
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 [crl] [crl]
RA 417,391 G→C A84P (GCC→CCC)  phoB → response regulator in two‑component regulatory system with PhoR
RA 702,066 G→C P229R (CCT→CGT)  nagA ← N‑acetylglucosamine‑6‑phosphate deacetylase
RA 1,158,384 G→A W172* (TGG→TGA)  ptsG → fused glucose‑specific PTS enzymes: IIB component/IIC component
RA 1,726,507 Δ1 bp coding (485/600 nt) nemR → transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated
MC JC 1,978,503 Δ776 bp insB1–insA insB1, insA
RA 2,132,787 A→C I204S (ATC→AGC)  wcaA ← putative glycosyl transferase
RA 2,509,477 C→T intergenic (‑53/‑151) glk ← / → yfeO glucokinase/putative ion channel protein
RA 2,977,594 +C coding (998/1032 nt) galR → galactose‑inducible d‑galactose regulon transcriptional repressor, autorepressor
MC JC 3,815,858 Δ82 bp [rph]–[rph] [rph], [rph]
MC JC 3,909,311 Δ774 bp [pstA]–[pstC] [pstA], [pstC]
JC 4,001,644 Δ5 bp coding (220‑224/951 nt) corA → magnesium/nickel/cobalt transporter
RA 4,184,542 C→A P1100Q (CCG→CAG)  rpoB → RNA polymerase, beta subunit

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 1293040 1306930 13891 49 [0] [0] 38 tdk–[yciU] tdk, insZ, insZ, insZ, adhE, ychE, oppA, oppB, oppC, oppD, oppF, [yciU]
* * ÷ NC_000913 2726648–2729154 2729154 1–2507 22 [20] [20] 22 rrlG 23S ribosomal RNA of rrnG operon
* * ÷ NC_000913 3423740–3424232 3424526–3424236 5–787 22 [21] [20] 23 [rrfD]–[rrlD] [rrfD], [rrlD]
* * ÷ NC_000913 4110727 4111537 811 24 [21] [21] 22 tpiA tpiA
* * ÷ NC_000913 4168671–4171676 4171676 1–3006 22 [21] [21] 22 [rrlB]–[rrfB] [rrlB], [rrfB]
* * ÷ NC_000913 4210102–4213074 4213074 1–2973 24 [21] [20] 23 [rrlE]–[rrfE] [rrlE], [rrfE]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 153986 =2 (0.040)92 (1.840) 51/282 0.0 97.9% coding (1441/2598 nt) htrE putative outer membrane usher protein
?NC_000913 = 275149 NA (NA)intergenic (‑32/‑176) insH1/mmuP IS5 transposase and trans‑activator/CP4‑6 prophage, putative S‑methylmethionine transporter
* ? NC_000913 = 1539891 (0.020)36 (0.720) 27/282 1.0 97.3% coding (1438/2598 nt) htrE putative outer membrane usher protein
?NC_000913 273955 = NA (NA)intergenic (+1/+146) ykfC/insH1 CP4‑6 prophage, conserved protein,Phage or Prophage Related/IS5 transposase and trans‑activator
* ? NC_000913 257908 =NA (NA)49 (0.980) 43/282 0.1 100% intergenic (+9/‑768) crl/crl pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers/pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers
?NC_000913 = 1293039 0 (0.000)intergenic (‑117/‑488) hns/tdk global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
* ? NC_000913 = 258674NA (NA)37 (0.750) 32/280 0.5 100% intergenic (+775/‑2) crl/crl pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers/pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers
?NC_000913 1306931 = 0 (0.000)coding (220/330 nt) yciU UPF0263 family protein
* ? NC_000913 = 609347NA (NA)40 (0.820) 35/274 0.3 97.6% intergenic (+170/+112) insL1/entD IS186 transposase/phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex
?NC_000913 1491900 = 1 (0.020)intergenic (+50/+22) ydcA/hokB putative periplasmic protein/toxic polypeptide, small
* ? NC_000913 1207790 =12 (0.240)34 (0.770) 29/250 0.5 75.9% coding (290/630 nt) stfP e14 prophage, uncharacterized protein
?NC_000913 1209619 = 11 (0.250)pseudogene (1/501 nt) stfE pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related
* ? NC_000913 = 120780513 (0.260)43 (0.970) 34/250 0.2 79.2% coding (305/630 nt) stfP e14 prophage, uncharacterized protein
?NC_000913 = 1209602 11 (0.250)pseudogene (18/501 nt) stfE pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related
* ? NC_000913 = 14919101 (0.020)58 (1.190) 55/274 0.0 98.4% intergenic (+60/+12) ydcA/hokB putative periplasmic protein/toxic polypeptide, small
?NC_000913 2514275 = NA (NA)intergenic (+33/‑54) nupC/insL1 nucleoside (except guanosine) transporter/IS186 transposase
* ? NC_000913 1979486 =0 (0.000)82 (1.640) 45/282 0.1 100% intergenic (‑271/‑267) insA/uspC IS1 repressor TnpA/universal stress protein
?NC_000913 2101749 = NA (NA)intergenic (‑5/+146) wbbL/insH1 pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator
* ? NC_000913 = 19794892 (0.040)50 (1.000) 41/282 0.2 96.2% intergenic (‑274/‑264) insA/uspC IS1 repressor TnpA/universal stress protein
?NC_000913 = 2290111 NA (NA)intergenic (‑32/+1) insH1/yejO IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system