breseq  version 0.32.0b  
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation freq annotation gene description
RA 468,126 Δ1 bp 39.1% coding (73/339 nt) glnK → nitrogen assimilation regulatory protein for GlnL, GlnE, and AmtB
RA 717,981 C→T 18.6% L630L (CTG→CTA)  kdpD ← fused sensory histidine kinase in two‑component regulatory system with KdpE: signal sensing protein
RA 982,560 T→A 30.9% intergenic (‑122/+481) ompF ← / ← asnS outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
RA 1,933,356 G→A 13.3% intergenic (+8/+123) pykA → / ← lpxM pyruvate kinase II/myristoyl‑acyl carrier protein (ACP)‑dependent acyltransferase
RA 2,219,065 G→A 13.9% Q16* (CAG→TAG)  yohC ← Yip1 family inner membrane protein
RA 2,249,251 A→G 19.1% N140D (AAT→GAT)  yeiL → putative transcriptional regulator
JC JC 2,400,257 IS5 (+) +4 bp 41.5% intergenic (‑137/‑780) lrhA ← / → alaA transcriptional repressor of flagellar, motility and chemotaxis genes/valine‑pyruvate aminotransferase 2
RA 2,420,328 G→A 70.4% intergenic (‑61/+160) hisJ ← / ← argT histidine/lysine/arginine/ornithine transporter subunit/lysine/arginine/ornithine transporter subunit
RA 2,420,329 C→A 73.2% intergenic (‑62/+159) hisJ ← / ← argT histidine/lysine/arginine/ornithine transporter subunit/lysine/arginine/ornithine transporter subunit
JC 2,420,338:1 +AATT 71.1% intergenic (‑71/+150) hisJ ← / ← argT histidine/lysine/arginine/ornithine transporter subunit/lysine/arginine/ornithine transporter subunit
RA 2,719,426 T→C 38.5% intergenic (‑321/+2) kgtP ← / ← rrfG alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon
RA 3,051,961 C→T 16.0% intergenic (‑192/+64) serA ← / ← rpiA D‑3‑phosphoglycerate dehydrogenase/ribose 5‑phosphate isomerase, constitutive
JC JC 3,178,254 IS5 (+) +4 bp 48.8% coding (56‑59/291 nt) yqiC → BMFP family putative fusogenic protein
RA 3,435,902 G→T 43.4% intergenic (‑72/+75) rpsM ← / ← rpmJ 30S ribosomal subunit protein S13/50S ribosomal subunit protein L36
RA 3,471,768 G→A 14.5% A30V (GCG→GTG)  slyD ← FKBP‑type peptidyl prolyl cis‑trans isomerase (rotamase)
RA 3,770,381 G→A 15.1% A119A (GCG→GCA)  yibL → ribosome‑associated DUF2810 family protein
RA 3,949,404 T→C 12.9% F238F (TTT→TTC)  ilvA → L‑threonine dehydratase, biosynthetic; also known as threonine deaminase
RA 3,953,437 Δ1 bp 29.4% pseudogene (178/243 nt) yifN ← PemK toxin family pseudogene
RA 3,960,035 C→A 19.0% R87S (CGC→AGC)  rho → transcription termination factor
RA 3,960,101 C→A 13.4% R109S (CGC→AGC)  rho → transcription termination factor
RA 3,969,337 G→T 35.0% E278* (GAG→TAG)  wecE → TDP‑4‑oxo‑6‑deoxy‑D‑glucose transaminase

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP009273 360104 =NA (NA)37 (1.920) 30/276 NT NA intergenic (‑38/+557) lacZ/lacI pseudogene, truncated/DNA‑binding transcriptional repressor
?CP009273 = 360286 NA (NA)intergenic (‑220/+375) lacZ/lacI pseudogene, truncated/DNA‑binding transcriptional repressor
* ? CP009273 1203246 =3 (0.160)8 (0.470) 8/244 NT 73.9% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?CP009273 1205075 = 3 (0.180)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? CP009273 = 12032613 (0.160)14 (0.820) 14/244 NT 83.2% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?CP009273 = 1205058 3 (0.180)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? CP009273 = 1391495NA (NA)11 (0.570) 9/276 NT 61.1% intergenic (+146/‑127) insH1/ynaJ IS5 transposase and trans‑activator/DUF2534 family putative inner membrane protein
?CP009273 = 1972751 7 (0.360)intergenic (‑297/‑483) flhD/uspC flagellar class II regulon transcriptional activator, with FlhC/universal stress protein
* ? CP009273 1972748 =8 (0.420)11 (0.570) 10/274 NT 57.9% intergenic (‑294/‑486) flhD/uspC flagellar class II regulon transcriptional activator, with FlhC/universal stress protein
?CP009273 = 2283592 NA (NA)noncoding (1/1195 nt) IS5 repeat region
* ? CP009273 2269338 =9 (0.470)9 (0.470) 8/276 NT 50.0% coding (587/1026 nt) yejE microcin C transporter YejABEF, permease subunit; ABC family
?CP009273 = 3577555 NA (NA)intergenic (+15/‑1) insB1/yrhA IS1 transposase B/pseudogene, interrupted by IS1E
* ? CP009273 = 226934611 (0.570)15 (0.780) 14/276 NT 57.7% coding (595/1026 nt) yejE microcin C transporter YejABEF, permease subunit; ABC family
?CP009273 3576788 = NA (NA)intergenic (+10/‑55) yrhA/insA pseudogene, interrupted by IS1E/IS1 repressor TnpA
* ? CP009273 4532499 =15 (0.780)3 (0.170) 3/258 NT 18.7% intergenic (+49/‑433) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
?CP009273 4532813 = 12 (0.670)intergenic (+363/‑119) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
* ? CP009273 = 453250716 (0.830)6 (0.330) 6/258 NT 30.8% intergenic (+57/‑425) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
?CP009273 = 4532803 12 (0.670)intergenic (+353/‑129) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)