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 1,299,499 Δ1,199 bp intergenic (+254/‑485) ychE → / → oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
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 2,316,391 T→C Y73H (TAC→CAC)  rcsB → response regulator in two‑component regulatory system with RcsC and YojN
RA 2,316,758 T→C V195A (GTC→GCC)  rcsB → response regulator in two‑component regulatory system with RcsC and YojN
RA 3,308,102 G→A A274V (GCA→GTA)  nlpI ← lipoprotein involved in osmotic sensitivity and filamentation
MC JC 3,527,656 Δ5 bp coding (1190‑1194/2136 nt) yrfF → putative RcsCDB‑response attenuator, inner membrane protein
MC JC 3,815,858 Δ82 bp [rph]–[rph] [rph], [rph]
JC 3,992,523 (CGGGC)2→1 coding (1372‑1376/2547 nt) cyaA → adenylate cyclase
JC 4,001,644 Δ5 bp coding (220‑224/951 nt) corA → magnesium/nickel/cobalt transporter
RA 4,103,655 Δ1 bp coding (1320/1374 nt) cpxA ← sensory histidine kinase in two‑component regulatory system with CpxR
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 366042 366435 394 17 [16] [15] 17 [lacZ]–[lacI] [lacZ], [lacI]
* * ÷ NC_000913 2533732 2536358 2627 17 [16] [16] 17 ptsH–crr ptsH, ptsI, crr
* * ÷ NC_000913 3423743–3424542 3424542 1–800 18 [16] [16] 17 [rrfD]–[rrlD] [rrfD], [rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 257908 =NA (NA)43 (0.960) 39/284 0.1 95.6% 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 2 (0.040)intergenic (‑117/‑488) hns/tdk global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
* ? NC_000913 1207790 =19 (0.420)15 (0.380) 14/252 2.1 41.2% coding (290/630 nt) stfP e14 prophage, uncharacterized protein
?NC_000913 1209619 = 26 (0.650)pseudogene (1/501 nt) stfE pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related
* ? NC_000913 = 120780519 (0.420)14 (0.350) 13/252 2.3 39.5% coding (305/630 nt) stfP e14 prophage, uncharacterized protein
?NC_000913 = 1209602 26 (0.650)pseudogene (18/501 nt) stfE pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related
* ? NC_000913 1293032 =2 (0.040)60 (1.330) 48/284 0.0 96.8% 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 1979486 =1 (0.020)48 (1.070) 33/284 0.3 98.0% 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 = 19794892 (0.040)55 (1.220) 29/284 0.5 96.5% 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