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 247 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 580,115 | 0 | C | T | 58.5% | 179.4 / inf | 258 | intergenic (+29/+136) | ybcW/ylcI | uncharacterized protein YbcW/DUF3950 domain‑containing protein YlcI |
| * | NC_000913 | 580,119 | 0 | A | G | 58.3% | 142.1 / inf | 259 | intergenic (+33/+132) | ybcW/ylcI | uncharacterized protein YbcW/DUF3950 domain‑containing protein YlcI |
| * | NC_000913 | 580,120 | 0 | C | T | 57.9% | 165.7 / inf | 261 | intergenic (+34/+131) | ybcW/ylcI | uncharacterized protein YbcW/DUF3950 domain‑containing protein YlcI |
| * | NC_000913 | 580,020 | 0 | G | A | 57.8% | 172.4 / inf | 275 | R47R (AGG→AGA) | ybcW | uncharacterized protein YbcW |
| * | NC_000913 | 1,634,724 | 0 | G | A | 55.1% | 33.6 / 226.0 | 167 | F54F (TTC→TTT) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,676 | 0 | A | G | 54.3% | 44.4 / 271.9 | 189 | D70D (GAT→GAC) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 579,811 | 0 | C | T | 54.1% | 81.8 / inf | 307 | intergenic (‑217/‑69) | ybcV/ybcW | DUF1398 domain‑containing protein YbcV/uncharacterized protein YbcW |
| * | NC_000913 | 579,671 | 0 | T | C | 54.0% | 47.0 / inf | 361 | intergenic (‑77/‑209) | ybcV/ybcW | DUF1398 domain‑containing protein YbcV/uncharacterized protein YbcW |
| * | NC_000913 | 579,385 | 0 | A | G | 54.0% | 109.8 / inf | 412 | N70N (AAT→AAC) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 1,634,699 | 0 | A | C | 54.0% | 39.8 / 236.1 | 176 | S63A (TCA→GCA) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 579,540 | 0 | T | C | 53.9% | 107.6 / inf | 400 | N19D (AAC→GAC) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 579,271 | 0 | G | A | 53.7% | 103.0 / inf | 340 | H108H (CAC→CAT) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 579,651 | 0 | C | T | 53.5% | 122.9 / inf | 381 | intergenic (‑57/‑229) | ybcV/ybcW | DUF1398 domain‑containing protein YbcV/uncharacterized protein YbcW |
| * | NC_000913 | 579,717 | 0 | A | C | 53.3% | 130.9 / inf | 396 | intergenic (‑123/‑163) | ybcV/ybcW | DUF1398 domain‑containing protein YbcV/uncharacterized protein YbcW |
| * | NC_000913 | 579,285 | 0 | T | C | 52.9% | 36.6 / inf | 345 | I104V (ATT→GTT) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 1,634,661 | 0 | C | G | 52.8% | 64.1 / inf | 197 | T75T (ACG→ACC) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 581,185 | 0 | C | T | 52.5% | ‑3.9 / 258.7 | 177 | L118L (CTG→TTG) | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 580,302 | 0 | C | T | 52.5% | 34.1 / inf | 282 | R48R (AGG→AGA) | ylcI | DUF3950 domain‑containing protein YlcI |
| * | NC_000913 | 579,502 | 0 | A | G | 52.4% | 54.1 / inf | 424 | N31N (AAT→AAC) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 579,457 | 0 | A | G | 51.4% | 28.4 / inf | 389 | I46I (ATT→ATC) | ybcV | DUF1398 domain‑containing protein YbcV |
| Marginal new junction evidence (lowest skew 10 of 194 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 2880584 | 110 (1.040) | 29 (0.270) | 25/592 | 3.2 | 20.9% | coding (465/675 nt) | casD | type I‑E CRISPR system Cascade subunit CasD |
| ? | NC_000913 | 4507459 = | NA (NA) | noncoding (1221/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | = 3584195 | NA (NA) | 27 (0.250) | 24/598 | 3.4 | 100% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 4542672 = | 0 (0.000) | intergenic (+39/‑443) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 1470516 | NA (NA) | 27 (0.250) | 22/594 | 3.8 | 22.5% | noncoding (1221/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | = 3560170 | 93 (0.880) | intergenic (+304/+452) | rtcR/glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG | |||||
| * | ? | NC_000913 | 2288919 = | NA (NA) | 22 (0.210) | 21/598 | 4.0 | 18.2% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 3727422 = | 99 (0.930) | coding (327/342 nt) | yiaB | PF05360 family inner membrane protein YiaB | |||||
| * | ? | NC_000913 | 1469296 = | NA (NA) | 22 (0.210) | 20/598 | 4.2 | 17.1% | noncoding (1/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | 2880583 = | 107 (1.000) | coding (466/675 nt) | casD | type I‑E CRISPR system Cascade subunit CasD | |||||
| * | ? | NC_000913 | = 566774 | 90 (0.840) | 45 (0.420) | 18/594 | 4.6 | 31.1% | pseudogene (91/93 nt) | renD | protein RenD |
| ? | NC_000913 | 568036 = | 110 (1.040) | pseudogene (2/213 nt) | renD | protein RenD | |||||
| * | ? | NC_000913 | 270541 = | NA (NA) | 21 (0.200) | 17/598 | 4.8 | 18.1% | noncoding (1/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | = 1855667 | 95 (0.890) | coding (305/981 nt) | ydjG | NADH‑dependent methylglyoxal reductase | |||||
| * | ? | NC_000913 | = 4606166 | 120 (1.120) | 11 (0.150) | 10/420 | 4.9 | 12.6% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 69 (0.920) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | 1431114 = | 127 (1.190) | 16 (0.150) | 16/598 | 5.1 | 11.2% | coding (2066/3363 nt) | stfR | putative prophage side tail fiber protein StfR |
| ? | NC_000913 | = 1470516 | NA (NA) | noncoding (1221/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | = 3648146 | 131 (1.230) | 13 (0.150) | 11/482 | 5.3 | 10.3% | intergenic (+2/‑148) | agrA/agrB | small RNA AgrA/small regulatory RNA AgrB |
| ? | NC_000913 | 3648378 = | 121 (1.410) | intergenic (+3/‑150) | agrB/arsR | small regulatory RNA AgrB/DNA‑binding transcriptional repressor ArsR | |||||