mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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 264 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 579,004 | 0 | C | T | 70.4% | 71.0 / 44.1 | 55 | intergenic (‑111/+180) | borD/ybcV | prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 1,097,494 | 0 | T | A | 69.2% | 14.6 / 16.0 | 27 | intergenic (+665/+71) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | NC_000913 | 580,020 | 0 | G | A | 67.2% | 78.3 / 60.8 | 68 | R47R (AGG→AGA) | ybcW | uncharacterized protein YbcW |
| * | NC_000913 | 1,429,160 | 0 | C | G | 67.0% | 136.6 / 95.6 | 95 | L38V (CTG→GTG) | stfR | putative prophage side tail fiber protein StfR |
| * | NC_000913 | 579,540 | 0 | T | C | 66.7% | 70.2 / 53.2 | 60 | N19D (AAC→GAC) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 1,429,171 | 0 | A | G | 66.3% | 122.9 / 96.7 | 101 | E41E (GAA→GAG) | stfR | putative prophage side tail fiber protein StfR |
| * | NC_000913 | 1,429,164 | 0 | C | G | 66.3% | 128.9 / 101.6 | 96 | A39G (GCC→GGC) | stfR | putative prophage side tail fiber protein StfR |
| * | NC_000913 | 580,115 | 0 | C | T | 66.2% | 75.5 / 69.9 | 71 | intergenic (+29/+136) | ybcW/ylcI | uncharacterized protein YbcW/DUF3950 domain‑containing protein YlcI |
| * | NC_000913 | 1,429,126 | 0 | A | C | 65.6% | 112.9 / 85.2 | 90 | A26A (GCA→GCC) | stfR | putative prophage side tail fiber protein StfR |
| * | NC_000913 | 580,302 | 0 | C | T | 65.3% | 90.8 / 67.6 | 77 | R48R (AGG→AGA) | ylcI | DUF3950 domain‑containing protein YlcI |
| * | NC_000913 | 1,429,128 | 0 | A | G | 64.8% | 85.8 / 88.1 | 90 | K27R (AAA→AGA) | stfR | putative prophage side tail fiber protein StfR |
| * | NC_000913 | 580,119 | 0 | A | G | 64.3% | 80.3 / 63.5 | 71 | intergenic (+33/+132) | ybcW/ylcI | uncharacterized protein YbcW/DUF3950 domain‑containing protein YlcI |
| * | NC_000913 | 1,429,111 | 0 | A | C | 64.3% | 83.3 / 91.9 | 84 | T21T (ACA→ACC) | stfR | putative prophage side tail fiber protein StfR |
| * | NC_000913 | 580,120 | 0 | C | T | 63.8% | 68.9 / 72.6 | 71 | intergenic (+34/+131) | ybcW/ylcI | uncharacterized protein YbcW/DUF3950 domain‑containing protein YlcI |
| * | NC_000913 | 1,429,724 | 0 | A | G | 62.8% | 140.3 / 176.6 | 174 | T226A (ACC→GCC) | stfR | putative prophage side tail fiber protein StfR |
| * | NC_000913 | 1,429,204 | 0 | C | T | 62.7% | 95.3 / 101.6 | 102 | D52D (GAC→GAT) | stfR | putative prophage side tail fiber protein StfR |
| * | NC_000913 | 1,429,114 | 0 | C | T | 62.4% | 68.3 / 95.1 | 86 | I22I (ATC→ATT) | stfR | putative prophage side tail fiber protein StfR |
| * | NC_000913 | 579,385 | 0 | A | G | 62.1% | 56.2 / 75.8 | 66 | N70N (AAT→AAC) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 579,099 | 0 | A | . | 62.1% | 23.3 / 114.1 | 59 | intergenic (‑206/+85) | borD/ybcV | prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 1,429,732 | 0 | G | A | 61.7% | 145.2 / 160.9 | 163 | K228K (AAG→AAA) | stfR | putative prophage side tail fiber protein StfR |
| Marginal new junction evidence (lowest skew 10 of 27 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 3722075 | NA (NA) | 7 (0.150) | 7/486 | 2.9 | 19.0% | noncoding (1443/1443 nt) | IS150 | repeat region |
| ? | NC_000913 | = 4598924 | 30 (0.630) | coding (518/2292 nt) | opgB | phosphoglycerol transferase I | |||||
| * | ? | NC_000913 | 3720633 = | NA (NA) | 7 (0.150) | 7/488 | 2.9 | 18.9% | noncoding (1/1443 nt) | IS150 | repeat region |
| ? | NC_000913 | 4598922 = | 30 (0.630) | coding (520/2292 nt) | opgB | phosphoglycerol transferase I | |||||
| * | ? | NC_000913 | = 3708541 | 32 (0.670) | 7 (0.150) | 7/468 | 2.9 | 16.5% | intergenic (‑836/+75) | dppA/proK | dipeptide ABC transporter periplasmic binding protein/tRNA‑Pro |
| ? | NC_000913 | 3708644 = | 40 (0.870) | noncoding (49/77 nt) | proK | tRNA‑Pro | |||||
| * | ? | NC_000913 | = 1307463 | 45 (0.950) | 7 (0.150) | 7/486 | 2.9 | 13.5% | coding (1183/1461 nt) | clsA | cardiolipin synthase A |
| ? | NC_000913 | = 2070271 | NA (NA) | noncoding (1/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 1307459 = | 45 (0.950) | 7 (0.150) | 7/486 | 2.9 | 13.5% | coding (1187/1461 nt) | clsA | cardiolipin synthase A |
| ? | NC_000913 | 1467910 = | NA (NA) | noncoding (1331/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 3186096 = | NA (NA) | 6 (0.130) | 6/488 | 3.2 | 22.2% | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 4361800 | 21 (0.440) | coding (135/1539 nt) | cadC | DNA‑binding transcriptional activator CadC | |||||
| * | ? | NC_000913 | 2288919 = | NA (NA) | 6 (0.130) | 6/488 | 3.2 | 13.6% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3844027 | 38 (0.800) | coding (64/1767 nt) | adeD | adenine deaminase | |||||
| * | ? | NC_000913 | = 1651548 | NA (NA) | 6 (0.130) | 6/488 | 3.2 | 21.4% | noncoding (706/706 nt) | IS2 | repeat region |
| ? | NC_000913 | = 1657379 | 22 (0.460) | coding (79/711 nt) | ynfC | PF06788 family lipoprotein YnfC | |||||
| * | ? | NC_000913 | = 1469240 | NA (NA) | 6 (0.130) | 6/488 | 3.2 | 13.6% | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 1599885 | 38 (0.800) | coding (325/1593 nt) | lsrK | autoinducer‑2 kinase | |||||
| * | ? | NC_000913 | = 1428794 | NA (NA) | 6 (0.130) | 6/486 | 3.2 | 40.1% | noncoding (1/1196 nt) | IS5 | repeat region |
| ? | NC_000913 | = 2470044 | 9 (0.190) | coding (914/1332 nt) | yfdI | serotype‑specific glucosyl transferase YfdI | |||||