breseq  version 0.33.1  revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation freq annotation gene description
RA 139,326 C→T 100% G634S (GGC→AGC)  gcd ← glucose dehydrogenase
MC JC 257,908 Δ776 bp 100% [crl] [crl]
JC JC 1,292,989 IS1 (+) +8 bp 100% intergenic (‑67/‑531) hns ← / → tdk global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
MC JC 1,299,499 Δ1,199 bp 100% intergenic (+254/‑485) ychE → / → oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
MC JC 1,978,503 Δ776 bp 100% insB1–insA insB1, insA
JC JC 1,979,486 IS5 (+) +4 bp 100% intergenic (‑271/‑264) insA ← / → uspC IS1 repressor TnpA/universal stress protein
RA 2,173,361 Δ2 bp 100% pseudogene (1‑2/442 nt) gatC ← pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC
RA 2,777,977 A→T 100% intergenic (+195/+169) ypjF → / ← ypjA CP4‑57 prophage; toxin of the YpjF‑YfjZ toxin‑antitoxin system/adhesin‑like autotransporter
RA 3,560,455:1 +G 100% intergenic (‑2/+1) glpR ← / ← glpR pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon
MC JC 3,815,859 Δ82 bp 100% [rph]–[rph] [rph], [rph]
JC JC 3,968,900 IS5 (–) +4 bp 100% coding (985‑988/1104 nt) wecA → UDP‑GlcNAc:undecaprenylphosphate GlcNAc‑1‑phosphate transferase
RA 4,184,543 C→A 100% P1100Q (CCG→CAG)  rpoB → RNA polymerase, beta subunit
RA 4,296,060 C→T 28.8% intergenic (+266/+376) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,380:1 +CG 100% intergenic (+586/+56) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,326,341 T→C 16.0% intergenic (‑600/+58) yjdN ← / ← yjdM metalloprotein superfamily protein/zinc‑ribbon family protein

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 283920 283935 16 2 [1] [1] 2 yagF CP4‑6 prophage; dehydratase family protein
* * ÷ NC_000913 300097 300114 18 2 [1] [1] 2 paoC PaoABC aldehyde oxidoreductase, Moco‑containing subunit
* * ÷ NC_000913 770905 770908 4 2 [0] [0] 2 mngB/cydA alpha‑mannosidase/cytochrome d terminal oxidase, subunit I
* * ÷ NC_000913 1211875 1212015 141 2 [1] [0] 2 [iraM] [iraM]
* * ÷ NC_000913 1640914 1640974 61 2 [0] [0] 2 essQ/cspB Qin prophage; putative S lysis protein/Qin prophage; cold shock protein
* * ÷ NC_000913 1795329 1795407 79 3 [1] [0] 2 ihfA integration host factor (IHF), DNA‑binding protein, alpha subunit
* * ÷ NC_000913 2282509 2282534 26 2 [0] [0] 2 [rplY] [rplY]
* * ÷ NC_000913 2385842 2385908 67 2 [0] [1] 3 [yfbL] [yfbL]
* * ÷ NC_000913 2386610 2386679 70 2 [1] [1] 2 yfbL putative M28A family peptidase
* * ÷ NC_000913 2469431 2469444 14 2 [0] [0] 2 gtrS serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
* * ÷ NC_000913 2470136 2470301 166 2 [0] [0] 2 gtrS serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
* * ÷ NC_000913 2590998 2591014 17 5 [0] [1] 5 ypfM/yffB stress‑induced small enterobacterial protein/putative ArsC family reductase
* * ÷ NC_000913 2591093 2591137 45 2 [0] [0] 2 ypfM/yffB stress‑induced small enterobacterial protein/putative ArsC family reductase
* * ÷ NC_000913 2624439 2624532 94 5 [0] [1] 3 ppk polyphosphate kinase, component of RNA degradosome
* * ÷ NC_000913 2888666 2888704 39 5 [1] [1] 2 cysI sulfite reductase, beta subunit, NAD(P)‑binding, heme‑binding
* * ÷ NC_000913 2903838 2903875 38 2 [0] [1] 2 ygcE/queE putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis
* * ÷ NC_000913 3185255 3185345 91 3 [1] [0] 2 yqiC/ygiL BMFP family putative fusogenic protein/putative fimbrial‑like adhesin protein
* * ÷ NC_000913 3361013 3361030 18 2 [0] [0] 2 gltD/gltF glutamate synthase, 4Fe‑4S protein, small subunit/periplasmic protein
* * ÷ NC_000913 3423845–3424232 3424439–3424239 8–595 2 [1] [1] 2 [rrlD] [rrlD]
* * ÷ NC_000913 3469809 3469921 113 6 [1] [0] 2 [chiA] [chiA]
* * ÷ NC_000913 3470031 3470051 21 2 [0] [1] 3 chiA/tufA periplasmic endochitinase/translation elongation factor EF‑Tu 1
* * ÷ NC_000913 3797078 3797108 31 2 [0] [1] 3 waaL O‑antigen ligase
* * ÷ NC_000913 3804437 3804494 58 2 [0] [1] 3 waaS lipopolysaccharide rhamnose:KdoIII transferase; lipopolysaccharide core biosynthesis protein
* * ÷ NC_000913 3804975 3805182 208 2 [1] [1] 2 [waaS]–[waaP] [waaS],[waaP]
* * ÷ NC_000913 4027044 4027094 51 2 [1] [1] 2 fre NAD(P)H‑flavin reductase
* * ÷ NC_000913 4304548 4304553 6 2 [0] [1] 3 ytcA/yjcS putative inner membrane efflux pump‑associated DUF1656 family protein/metallo‑beta‑lactamase superfamily protein
* * ÷ NC_000913 4472201 4472256 56 4 [1] [1] 4 pyrB aspartate carbamoyltransferase, catalytic subunit
* * ÷ NC_000913 4571930 4571970 41 2 [0] [1] 2 yjiS/yjiT DUF1127 family protein/pseudogene
* * ÷ NC_000913 4571999 4572011 13 2 [1] [0] 6 yjiS/yjiT DUF1127 family protein/pseudogene

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 1207790 =5 (0.270)19 (1.130) 18/348 NT 85.2% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 2 (0.120)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 12078054 (0.220)10 (0.600) 10/348 NT 77.9% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 2 (0.120)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 3182319 =31 (1.690)3 (0.170) 3/366 NT 10.0% coding (89/789 nt) ygiD 4,5‑ DOPA‑extradiol‑dioxygenase
?NC_000913 3182392 = 24 (1.360)coding (16/789 nt) ygiD 4,5‑ DOPA‑extradiol‑dioxygenase