mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 205 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 807,343 | 0 | C | G | 66.7% | 26.9 / 21.0 | 24 | intergenic (‑62/+90) | ybhC/ybhB | outer membrane lipoprotein YbhC/putative kinase inhibitor |
| * | NC_000913 | 579,811 | 0 | C | T | 53.4% | 67.6 / inf | 268 | intergenic (‑217/‑69) | ybcV/ybcW | DUF1398 domain‑containing protein YbcV/uncharacterized protein YbcW |
| * | NC_000913 | 578,831 | 0 | T | C | 52.8% | 53.2 / inf | 303 | T21T (ACA→ACG) | borD | prophage lipoprotein BorD |
| * | NC_000913 | 579,385 | 0 | A | G | 52.3% | 27.6 / inf | 308 | N70N (AAT→AAC) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 578,809 | 0 | T | C | 52.0% | 18.6 / inf | 279 | T29A (ACA→GCA) | borD | prophage lipoprotein BorD |
| * | NC_000913 | 579,285 | 0 | T | C | 51.9% | 6.0 / inf | 285 | I104V (ATT→GTT) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 579,004 | 0 | C | T | 51.8% | 50.5 / inf | 298 | intergenic (‑111/+180) | borD/ybcV | prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 578,811 | 0 | T | G | 51.6% | 62.7 / inf | 278 | Q28P (CAG→CCG) | borD | prophage lipoprotein BorD |
| * | NC_000913 | 579,671 | 0 | T | C | 51.1% | ‑6.5 / inf | 314 | intergenic (‑77/‑209) | ybcV/ybcW | DUF1398 domain‑containing protein YbcV/uncharacterized protein YbcW |
| * | NC_000913 | 579,457 | 0 | A | G | 51.0% | 0.2 / inf | 314 | I46I (ATT→ATC) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 579,502 | 0 | A | G | 50.9% | 10.3 / inf | 342 | N31N (AAT→AAC) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 580,115 | 0 | C | T | 50.9% | 32.7 / inf | 226 | intergenic (+29/+136) | ybcW/ylcI | uncharacterized protein YbcW/DUF3950 domain‑containing protein YlcI |
| * | NC_000913 | 579,540 | 0 | T | C | 50.9% | ‑6.6 / inf | 345 | N19D (AAC→GAC) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 579,271 | 0 | G | A | 50.7% | 13.8 / inf | 275 | H108H (CAC→CAT) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 579,099 | 0 | A | . | 50.7% | inf / inf | 284 | intergenic (‑206/+85) | borD/ybcV | prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 579,717 | 0 | A | C | 50.6% | 47.9 / inf | 346 | intergenic (‑123/‑163) | ybcV/ybcW | DUF1398 domain‑containing protein YbcV/uncharacterized protein YbcW |
| * | NC_000913 | 580,120 | 0 | C | T | 50.4% | 25.3 / inf | 227 | intergenic (+34/+131) | ybcW/ylcI | uncharacterized protein YbcW/DUF3950 domain‑containing protein YlcI |
| * | NC_000913 | 581,337 | 0 | G | A | 50.3% | 13.0 / 249.2 | 161 | L168L (CTG→CTA) ‡ | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 580,119 | 0 | A | G | 50.2% | 16.4 / inf | 227 | intergenic (+33/+132) | ybcW/ylcI | uncharacterized protein YbcW/DUF3950 domain‑containing protein YlcI |
| * | NC_000913 | 581,335 | 0 | C | A | 50.0% | 18.3 / 230.6 | 162 | L168M (CTG→ATG) ‡ | nohD | putative DNA‑packaging protein NohD |
| Marginal new junction evidence (lowest skew 10 of 12 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 361522 = | 1 (0.010) | 55 (0.510) | 29/584 | 3.0 | 56.4% | coding (339/612 nt) | lacA | galactoside O‑acetyltransferase |
| ? | NC_000913 | = 1429390 | 84 (0.780) | coding (342/3363 nt) | stfR | putative prophage side tail fiber protein StfR | |||||
| * | ? | NC_000913 | = 3648146 | 388 (3.510) | 25 (0.280) | 21/482 | 3.4 | 7.3% | intergenic (+2/‑148) | agrA/agrB | small RNA AgrA/small regulatory RNA AgrB |
| ? | NC_000913 | 3648378 = | 320 (3.590) | intergenic (+3/‑150) | agrB/arsR | small regulatory RNA AgrB/DNA‑binding transcriptional repressor ArsR | |||||
| * | ? | NC_000913 | = 781222 | 75 (0.680) | 10 (0.120) | 10/446 | 6.0 | 14.3% | noncoding (76/76 nt) | lysY | tRNA‑Lys |
| ? | NC_000913 | 781653 = | 64 (0.780) | intergenic (+1/‑432) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | = 4606166 | 117 (1.060) | 8 (0.100) | 8/420 | 6.4 | 9.6% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 68 (0.880) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | = 1287329 | 75 (0.680) | 10 (0.130) | 8/424 | 6.5 | 16.4% | intergenic (‑1/+209) | tyrV/tyrT | tRNA‑Tyr/tRNA‑Tyr |
| ? | NC_000913 | 1287624 = | 49 (0.630) | intergenic (‑2/+158) | tyrT/purU | tRNA‑Tyr/formyltetrahydrofolate deformylase | |||||
| * | ? | NC_000913 | = 566774 | 115 (1.040) | 41 (0.370) | 10/594 | 7.8 | 27.0% | pseudogene (91/93 nt) | renD | protein RenD |
| ? | NC_000913 | 568036 = | 107 (0.980) | pseudogene (2/213 nt) | renD | protein RenD | |||||
| * | ? | NC_000913 | = 1286906 | 79 (0.720) | 9 (0.090) | 8/558 | 8.2 | 11.6% | coding (198/276 nt) | ychS | putative uncharacterized protein YchS |
| ? | NC_000913 | 1287557 = | 63 (0.610) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 2947467 | 92 (0.830) | 4 (0.050) | 4/432 | 8.7 | 5.4% | intergenic (+4/‑30) | metZ/metW | tRNA‑Met/tRNA‑Met |
| ? | NC_000913 | 2947688 = | 74 (0.930) | intergenic (+5/+69) | metV/amiC | tRNA‑Met/N‑acetylmuramoyl‑L‑alanine amidase C | |||||
| * | ? | NC_000913 | = 3648150 | 392 (3.550) | 8 (0.070) | 7/592 | 9.1 | 2.0% | intergenic (+6/‑144) | agrA/agrB | small RNA AgrA/small regulatory RNA AgrB |
| ? | NC_000913 | 3648382 = | 408 (3.730) | intergenic (+7/‑146) | agrB/arsR | small regulatory RNA AgrB/DNA‑binding transcriptional repressor ArsR | |||||
| * | ? | NC_000913 | 1096961 = | 79 (0.720) | 4 (0.050) | 3/438 | 9.5 | 5.8% | intergenic (+132/+604) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| ? | NC_000913 | = 1097503 | 71 (0.880) | intergenic (+674/+62) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser | |||||