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

Predicted mutations
evidence position mutation freq annotation gene description
MC JC 257,908 Δ776 bp 100% [crl] [crl]
JC JC 458,790 IS186 (–) +6 bp :: Δ1 bp 100% intergenic (+90/‑93) clpX → / → lon ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La
JC 628,060 Δ3 bp 5.6% coding (367‑369/858 nt) entB → isochorismatase
RA 1,196,305 C→T 100% R395C (CGT→TGT)  icd → isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase
JC JC 1,293,032 IS1 (–) +8 bp 100% intergenic (‑110/‑488) hns ← / → tdk global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
JC JC 1,979,486 IS5 (+) +4 bp 100% intergenic (‑271/‑264) insA ← / → uspC IS1 repressor TnpA/universal stress protein
RA 2,132,787 A→C 100% I204S (ATC→AGC)  wcaA ← putative glycosyl transferase
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 2,415,466 Δ1 bp 7.0% coding (720/2145 nt) pta → phosphate acetyltransferase
RA 2,707,558 Δ1 bp 100% coding (244/480 nt) rseC ← SoxR iron‑sulfur cluster reduction factor component
RA 3,213,429 A→C 6.8% N128T (AAC→ACC)  rpoD → RNA polymerase, sigma 70 (sigma D) factor
RA 3,213,434 G→A 50.9% V130I (GTT→ATT)  rpoD → RNA polymerase, sigma 70 (sigma D) factor
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 4,001,645 Δ5 bp 100% coding (220‑224/951 nt) corA → magnesium/nickel/cobalt transporter
JC JC 4,049,922 IS5 (–) +4 bp 100% noncoding (24‑27/109 nt) spf → Spot 42 sRNA antisense regulator of galK translation, Hfq‑dependent
RA 4,184,543 C→A 100% P1100Q (CCG→CAG)  rpoB → RNA polymerase, beta subunit
RA 4,296,060 C→T 13.5% intergenic (+266/+376) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,190 A→G 14.8% intergenic (+396/+246) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,191 A→C 14.0% intergenic (+397/+245) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,268 T→C 22.6% intergenic (+474/+168) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,286 C→T 11.0% intergenic (+492/+150) 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 4,354,908 A→T 7.5% intergenic (‑191/+46) lysU ← / ← dtpC lysine tRNA synthetase, inducible/dipeptide and tripeptide permease

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 3423828–3424402 3424402 1–575 53 [50] [50] 53 [rrlD] [rrlD]
* * ÷ NC_000913 4233715 4235570 1856 54 [50] [51] 56 pgi pgi

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 = 381689NA (NA)11 (0.090) 10/486 NT NA noncoding (430/1331 nt) IS2 repeat region
?NC_000913 = 381743 NA (NA)noncoding (484/1331 nt) IS2 repeat region
* ? NC_000913 1207790 =67 (0.510)92 (0.750) 69/472 NT 65.8% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 33 (0.270)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 120780561 (0.470)71 (0.580) 51/472 NT 61.2% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 33 (0.270)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 12994980 (0.000)74 (0.570) 54/496 NT 100% 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 = 19785020 (0.000)51 (0.400) 39/488 NT 100% intergenic (‑305/+16) flhD/insB1 flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B
?NC_000913 1979279 = 0 (0.000)intergenic (‑64/‑474) insA/uspC IS1 repressor TnpA/universal stress protein
* ? NC_000913 = 2647282129 (0.980)7 (0.060) 7/484 NT 5.5% coding (44/2313 nt) pbpC penicillin‑insensitive murein repair transglycosylase; inactive transpeptidase domain protein
?NC_000913 = 2647351 116 (0.920)coding (4937/4962 nt) yfhM bacterial alpha2‑macroglobulin colonization factor ECAM; anti‑host protease defense factor; periplasmic inner membrane‑anchored lipoprotein
* ? NC_000913 4295832 =NA (NA)8 (0.070) 3/426 NT NA intergenic (+38/+604) gltP/yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
?NC_000913 = 4296394 NA (NA)noncoding (560/600 nt) RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites
* ? NC_000913 4542682 =40 (0.310)9 (0.070) 9/486 NT 14.0% intergenic (+49/‑433) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
?NC_000913 4542996 = 72 (0.570)intergenic (+363/‑119) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
* ? NC_000913 = 454269038 (0.290)9 (0.070) 8/486 NT 14.2% intergenic (+57/‑425) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
?NC_000913 = 4542986 72 (0.570)intergenic (+353/‑129) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)