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

Predicted mutations
evidence position mutation annotation gene description
JC JC 542,271 IS5 (–) +4 bp coding (136‑139/1668 nt) fdrA → putative NAD(P)‑binding acyl‑CoA synthetase
RA 1,191,676 C→T H366H (CAC→CAT)  icd → e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA 1,191,688 C→T T370T (ACC→ACT)  icd → e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA 1,191,701 T→C L375M (TTA→CTG)  icd → e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA 1,191,703 A→G L375M (TTA→CTG)  icd → e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA 1,191,733 C→T N385N (AAC→AAT)  icd → e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA 1,191,736 G→C A386A (GCG→GCC)  icd → e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA 1,191,739 A→G K387K (AAA→AAG)  icd → e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA 1,191,748 C→T T390T (ACC→ACT)  icd → e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA 1,909,455 G→A Q113* (CAG→TAG)  proQ ← RNA chaperone, putative ProP translation regulator
JC JC 2,400,257 IS5 (+) +4 bp intergenic (‑137/‑780) lrhA ← / → alaA transcriptional repressor of flagellar, motility and chemotaxis genes/valine‑pyruvate aminotransferase 2
MC JC 2,420,337 Δ120 bp intergenic (‑70/+32) hisJ ← / ← argT histidine/lysine/arginine/ornithine transporter subunit/lysine/arginine/ornithine transporter subunit
RA 2,420,470 C→A intergenic (‑203/+18) hisJ ← / ← argT histidine/lysine/arginine/ornithine transporter subunit/lysine/arginine/ornithine transporter subunit
JC JC 3,178,254 IS5 (+) +4 bp coding (56‑59/291 nt) yqiC → BMFP family putative fusogenic protein

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ CP009273 1191760 1206891 15132 15 [12] [14] 16 [icd]–[icdC] 25 genes
[icd], ymfD, ymfE, lit, intE, xisE, ymfI, ymfJ, cohE, croE, ymfL, ymfM, oweE, aaaE, ymfR, beeE, jayE, ymfQ, stfP, tfaP, tfaE, stfE, pinE, mcrA, [icdC]
* * ÷ CP009273 2084546 2085918 1373 16 [14] [14] 15 [hisG]–[hisC] [hisG], hisD, [hisC]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP009273 360104 =NA (NA)45 (1.060) 38/296 0.1 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 454243 =3 (0.070)43 (1.030) 35/290 0.2 93.6% intergenic (+87/‑101) clpX/lon ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La
?CP009273 603467 = NA (NA)intergenic (+23/‑54) hokE/insL1 toxic polypeptide, small/IS186 transposase
* ? CP009273 = 4542553 (0.070)37 (0.890) 31/288 0.4 92.7% intergenic (+99/‑89) clpX/lon ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La
?CP009273 = 604803 NA (NA)intergenic (+170/+112) insL1/entD IS186 transposase/phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex
* ? CP009273 = 453250724 (0.560)11 (0.280) 11/278 2.8 31.2% intergenic (+57/‑425) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
?CP009273 = 4532803 26 (0.650)intergenic (+353/‑129) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)