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]
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 2,509,495 C→G intergenic (‑71/‑133) glk ← / → yfeO glucokinase/putative ion channel protein
RA 3,088,093 T→A intergenic (+235/‑189) metK → / → galP S‑adenosylmethionine synthetase/D‑galactose transporter
MC JC 3,815,858 Δ82 bp [rph]–[rph] [rph], [rph]
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 2533729 2536367 2639 31 [30] [30] 31 ptsH–crr ptsH, ptsI, crr

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 257908 =NA (NA)58 (0.840) 55/284 0.1 90.6% 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 6 (0.090)intergenic (‑117/‑488) hns/tdk global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
* ? NC_000913 1207790 =7 (0.100)52 (0.850) 46/252 0.2 87.2% coding (290/630 nt) stfP e14 prophage, uncharacterized protein
?NC_000913 1209619 = 9 (0.150)pseudogene (1/501 nt) stfE pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related
* ? NC_000913 = 12078056 (0.090)49 (0.800) 41/252 0.4 87.2% coding (305/630 nt) stfP e14 prophage, uncharacterized protein
?NC_000913 = 1209602 9 (0.150)pseudogene (18/501 nt) stfE pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related
* ? NC_000913 1293032 =5 (0.070)91 (1.320) 71/284 0.0 94.8% intergenic (‑110/‑495) hns/tdk global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
?NC_000913 = 1979270 NA (NA)intergenic (‑55/‑483) insA/uspC IS1 repressor TnpA/universal stress protein
* ? NC_000913 = 12994981 (0.010)70 (1.050) 57/276 0.1 99.3% intergenic (+253/‑1684) ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
?NC_000913 1300698 = 0 (0.000)intergenic (+1453/‑484) ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
* ? NC_000913 1979486 =1 (0.010)99 (1.440) 60/284 0.1 99.0% 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 = 19794894 (0.060)128 (1.860) 61/284 0.1 97.0% 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
* ? NC_000913 2024155 =3 (0.040)70 (1.020) 59/284 0.1 95.9% coding (188/624 nt) rcsA transcriptional regulator of colanic acid capsular biosynthesis
?NC_000913 2101749 = NA (NA)intergenic (‑5/+146) wbbL/insH1 pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator
* ? NC_000913 = 20241582 (0.030)53 (0.770) 44/284 0.5 96.4% coding (191/624 nt) rcsA transcriptional regulator of colanic acid capsular biosynthesis
?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
* ? NC_000913 2262020 =5 (0.070)69 (1.020) 54/278 0.1 93.4% coding (344/939 nt) fruK fructose‑1‑phosphate kinase
?NC_000913 = 2515611 NA (NA)intergenic (+170/+30) insL1/yfeA IS186 transposase/putative diguanylate cyclase
* ? NC_000913 = 226203011 (0.160)46 (0.670) 41/282 0.7 80.8% coding (334/939 nt) fruK fructose‑1‑phosphate kinase
?NC_000913 2514274 = NA (NA)intergenic (+32/‑55) nupC/insL1 nucleoside (except guanosine) transporter/IS186 transposase
* ? NC_000913 2288917 =NA (NA)66 (0.960) 53/284 0.2 90.4% intergenic (‑5/+146) yejO/insH1 pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system/IS5 transposase and trans‑activator
?NC_000913 3526447 = 7 (0.100)intergenic (‑300/‑20) nudE/yrfF adenosine nucleotide hydrolase, Ap3A/Ap2A/ADP‑ribose/NADH hydrolase/putative RcsCDB‑response attenuator, inner membrane protein
* ? NC_000913 = 2290110NA (NA)67 (0.980) 55/282 0.1 97.1% intergenic (‑31/+2) insH1/yejO IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system
?NC_000913 = 3526451 2 (0.030)intergenic (‑304/‑16) nudE/yrfF adenosine nucleotide hydrolase, Ap3A/Ap2A/ADP‑ribose/NADH hydrolase/putative RcsCDB‑response attenuator, inner membrane protein
* ? NC_000913 3845530 =67 (0.970)61 (0.950) 54/264 0.1 48.6% coding (1568/1767 nt) adeD cryptic adenine deaminase
?NC_000913 = 3992759 67 (1.050)coding (1608/2547 nt) cyaA adenylate cyclase