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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) | |||||||||||
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seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
* | NC_000913 | 1,429,404 | 0 | C | T | 58.9% | 38.4 / 58.8 | 56 | A119V (GCG→GTG) | stfR | putative prophage side tail fiber protein StfR |
* | NC_000913 | 1,429,364 | 0 | T | C | 58.8% | 33.2 / 54.5 | 51 | F106L (TTT→CTT) | stfR | putative prophage side tail fiber protein StfR |
* | NC_000913 | 1,429,416 | 0 | A | G | 57.9% | 35.8 / 64.7 | 57 | N123S (AAC→AGC) ‡ | stfR | putative prophage side tail fiber protein StfR |
* | NC_000913 | 1,429,417 | 0 | C | T | 57.9% | 34.1 / 61.4 | 57 | N123N (AAC→AAT) ‡ | stfR | putative prophage side tail fiber protein StfR |
* | NC_000913 | 1,429,360 | 0 | C | T | 57.7% | 21.1 / 62.3 | 52 | R104R (CGC→CGT) | stfR | putative prophage side tail fiber protein StfR |
* | NC_000913 | 1,429,425 | 0 | C | A | 56.9% | 26.6 / 60.9 | 58 | A126D (GCC→GAC) | stfR | putative prophage side tail fiber protein StfR |
* | NC_000913 | 1,429,454 | 0 | A | G | 55.4% | 18.8 / 66.4 | 59 | T136A (ACA→GCA) | stfR | putative prophage side tail fiber protein StfR |
* | NC_000913 | 1,429,435 | 0 | G | A | 55.2% | 17.1 / 67.7 | 58 | K129K (AAG→AAA) | stfR | putative prophage side tail fiber protein StfR |
* | NC_000913 | 1,429,537 | 0 | G | A | 54.8% | 25.2 / 78.4 | 62 | A163A (GCG→GCA) | stfR | putative prophage side tail fiber protein StfR |
* | NC_000913 | 1,429,543 | 0 | G | A | 54.8% | 20.6 / 77.1 | 62 | S165S (TCG→TCA) | stfR | putative prophage side tail fiber protein StfR |
* | NC_000913 | 580,302 | 0 | C | T | 54.8% | 2.1 / 50.2 | 44 | R48R (AGG→AGA) | ylcI | DUF3950 domain‑containing protein YlcI |
* | NC_000913 | 1,429,534 | 0 | C | T | 54.7% | 14.8 / 76.6 | 64 | A162A (GCC→GCT) | stfR | putative prophage side tail fiber protein StfR |
* | NC_000913 | 1,635,974 | 0 | T | G | 54.3% | ‑1.5 / 37.4 | 35 | I132L (ATC→CTC) | nohA | putative prophage DNA‑packaging protein NohA |
* | NC_000913 | 1,429,522 | 0 | A | C | 54.0% | 6.4 / 78.8 | 63 | S158S (TCA→TCC) | stfR | putative prophage side tail fiber protein StfR |
* | NC_000913 | 1,429,708 | 0 | A | G | 53.7% | 12.0 / 92.2 | 67 | T220T (ACA→ACG) | stfR | putative prophage side tail fiber protein StfR |
* | NC_000913 | 1,429,550 | 0 | T | G | 53.3% | 19.9 / 61.9 | 61 | S168A (TCA→GCA) | stfR | putative prophage side tail fiber protein StfR |
* | NC_000913 | 1,429,558 | 0 | T | C | 53.3% | ‑0.0 / 74.9 | 61 | S170S (TCT→TCC) | stfR | putative prophage side tail fiber protein StfR |
* | NC_000913 | 1,636,068 | 0 | T | C | 53.3% | ‑0.6 / 65.2 | 45 | K100K (AAA→AAG) | nohA | putative prophage DNA‑packaging protein NohA |
* | NC_000913 | 578,811 | 0 | T | G | 52.9% | ‑5.6 / 76.1 | 52 | Q28P (CAG→CCG) | borD | prophage lipoprotein BorD |
* | NC_000913 | 1,429,732 | 0 | G | A | 52.9% | 9.6 / 93.1 | 71 | K228K (AAG→AAA) | stfR | putative prophage side tail fiber protein StfR |
Marginal new junction evidence (sorted from low to high skew) | |||||||||||
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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 |