breseq  version 0.39.0  
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence (highest frequency 20 of 208 shown, sorted by frequency from high to low)
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,429,4040CT58.9% 38.4 / 58.8 56A119V (GCG→GTG) stfRputative prophage side tail fiber protein StfR
*NC_0009131,429,3640TC58.8% 33.2 / 54.5 51F106L (TTT→CTT) stfRputative prophage side tail fiber protein StfR
*NC_0009131,429,4160AG57.9% 35.8 / 64.7 57N123S (AAC→AGC) ‡stfRputative prophage side tail fiber protein StfR
*NC_0009131,429,4170CT57.9% 34.1 / 61.4 57N123N (AAC→AAT) ‡stfRputative prophage side tail fiber protein StfR
*NC_0009131,429,3600CT57.7% 21.1 / 62.3 52R104R (CGC→CGTstfRputative prophage side tail fiber protein StfR
*NC_0009131,429,4250CA56.9% 26.6 / 60.9 58A126D (GCC→GAC) stfRputative prophage side tail fiber protein StfR
*NC_0009131,429,4540AG55.4% 18.8 / 66.4 59T136A (ACA→GCA) stfRputative prophage side tail fiber protein StfR
*NC_0009131,429,4350GA55.2% 17.1 / 67.7 58K129K (AAG→AAAstfRputative prophage side tail fiber protein StfR
*NC_0009131,429,5370GA54.8% 25.2 / 78.4 62A163A (GCG→GCAstfRputative prophage side tail fiber protein StfR
*NC_0009131,429,5430GA54.8% 20.6 / 77.1 62S165S (TCG→TCAstfRputative prophage side tail fiber protein StfR
*NC_000913580,3020CT54.8% 2.1 / 50.2 44R48R (AGG→AGAylcIDUF3950 domain‑containing protein YlcI
*NC_0009131,429,5340CT54.7% 14.8 / 76.6 64A162A (GCC→GCTstfRputative prophage side tail fiber protein StfR
*NC_0009131,635,9740TG54.3% ‑1.5 / 37.4 35I132L (ATC→CTC) nohAputative prophage DNA‑packaging protein NohA
*NC_0009131,429,5220AC54.0% 6.4 / 78.8 63S158S (TCA→TCCstfRputative prophage side tail fiber protein StfR
*NC_0009131,429,7080AG53.7% 12.0 / 92.2 67T220T (ACA→ACGstfRputative prophage side tail fiber protein StfR
*NC_0009131,429,5500TG53.3% 19.9 / 61.9 61S168A (TCA→GCA) stfRputative prophage side tail fiber protein StfR
*NC_0009131,429,5580TC53.3% ‑0.0 / 74.9 61S170S (TCT→TCCstfRputative prophage side tail fiber protein StfR
*NC_0009131,636,0680TC53.3% ‑0.6 / 65.2 45K100K (AAA→AAGnohAputative prophage DNA‑packaging protein NohA
*NC_000913578,8110TG52.9% ‑5.6 / 76.1 52Q28P (CAG→CCG) borDprophage lipoprotein BorD
*NC_0009131,429,7320GA52.9% 9.6 / 93.1 71K228K (AAG→AAAstfRputative prophage side tail fiber protein StfR

Marginal new junction evidence (sorted from low to high skew)
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 4542682 =37 (0.910)3 (0.080) 3/468 2.8 8.4% intergenic (+49/‑433) fimE/fimA regulator for fimA/type 1 fimbriae major subunit
?NC_000913 4542996 = 30 (0.760)intergenic (+363/‑119) fimE/fimA regulator for fimA/type 1 fimbriae major subunit