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 272 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 1,097,494 | 0 | T | A | 73.0% | 122.7 / 56.7 | 69 | intergenic (+665/+71) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | NC_000913 | 1,196,232 | 0 | C | T | 69.9% | 78.3 / 56.8 | 73 | T370T (ACC→ACT) | icd | isocitrate dehydrogenase |
| * | NC_000913 | 1,196,220 | 0 | C | T | 69.6% | 89.2 / 58.8 | 79 | H366H (CAC→CAT) | icd | isocitrate dehydrogenase |
| * | NC_000913 | 1,196,245 | 0 | T | C | 69.4% | 66.2 / 60.4 | 72 | L375L (TTA→CTA) ‡ | icd | isocitrate dehydrogenase |
| * | NC_000913 | 1,196,247 | 0 | A | G | 69.4% | 71.5 / 57.1 | 72 | L375L (TTA→TTG) ‡ | icd | isocitrate dehydrogenase |
| * | NC_000913 | 1,196,277 | 0 | C | T | 61.8% | 30.6 / 67.7 | 68 | N385N (AAC→AAT) | icd | isocitrate dehydrogenase |
| * | NC_000913 | 1,196,280 | 0 | G | C | 61.2% | 10.9 / 83.4 | 68 | A386A (GCG→GCC) | icd | isocitrate dehydrogenase |
| * | NC_000913 | 1,196,283 | 0 | A | G | 60.9% | 15.6 / 81.4 | 69 | K387K (AAA→AAG) | icd | isocitrate dehydrogenase |
| * | NC_000913 | 1,196,292 | 0 | C | T | 60.6% | 22.1 / 69.0 | 66 | T390T (ACC→ACT) | icd | isocitrate dehydrogenase |
| * | NC_000913 | 578,809 | 0 | T | C | 60.4% | 209.9 / inf | 308 | T29A (ACA→GCA) | borD | prophage lipoprotein BorD |
| * | NC_000913 | 578,811 | 0 | T | G | 60.1% | 261.1 / inf | 308 | Q28P (CAG→CCG) | borD | prophage lipoprotein BorD |
| * | NC_000913 | 578,831 | 0 | T | C | 59.6% | 199.5 / inf | 327 | T21T (ACA→ACG) | borD | prophage lipoprotein BorD |
| * | NC_000913 | 579,099 | 0 | A | . | 58.9% | 171.2 / inf | 333 | intergenic (‑206/+85) | borD/ybcV | prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 1,634,724 | 0 | G | A | 58.9% | ‑2.3 / 192.5 | 158 | F54F (TTC→TTT) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,196,304 | 0 | G | A | 58.1% | ‑4.2 / 72.6 | 62 | E394E (GAG→GAA) | icd | isocitrate dehydrogenase |
| * | NC_000913 | 580,115 | 0 | C | T | 57.5% | 209.6 / 315.9 | 259 | intergenic (+29/+136) | ybcW/ylcI | uncharacterized protein YbcW/DUF3950 domain‑containing protein YlcI |
| * | NC_000913 | 1,634,699 | 0 | A | C | 57.0% | ‑3.6 / 209.3 | 172 | S63A (TCA→GCA) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 579,004 | 0 | C | T | 56.9% | 217.4 / inf | 343 | intergenic (‑111/+180) | borD/ybcV | prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 578,729 | 0 | A | G | 56.7% | 129.6 / inf | 312 | A55A (GCT→GCC) | borD | prophage lipoprotein BorD |
| * | NC_000913 | 580,119 | 0 | A | G | 56.6% | 125.8 / inf | 258 | intergenic (+33/+132) | ybcW/ylcI | uncharacterized protein YbcW/DUF3950 domain‑containing protein YlcI |
| Marginal new junction evidence (lowest skew 10 of 26 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 566774 | 119 (1.110) | 67 (0.630) | 24/594 | 3.5 | 35.5% | pseudogene (91/93 nt) | renD | protein RenD |
| ? | NC_000913 | 568036 = | 125 (1.170) | pseudogene (2/213 nt) | renD | protein RenD | |||||
| * | ? | NC_000913 | 1207790 = | 4 (0.040) | 14 (0.140) | 14/566 | 5.4 | 63.9% | coding (290/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | 1209619 = | 12 (0.120) | intergenic (‑500/‑66) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 696741 | 108 (1.010) | 10 (0.130) | 9/442 | 5.6 | 11.4% | intergenic (‑1/+15) | metU/glnW | tRNA‑Met/tRNA‑Gln |
| ? | NC_000913 | 697135 = | 75 (0.950) | intergenic (‑2/+378) | metT/asnB | tRNA‑Met/asparagine synthetase B | |||||
| * | ? | NC_000913 | = 1207805 | 5 (0.050) | 15 (0.150) | 13/566 | 5.7 | 68.6% | coding (305/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | = 1209602 | 9 (0.090) | intergenic (‑483/‑83) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 781222 | 83 (0.770) | 7 (0.090) | 6/446 | 6.9 | 8.6% | noncoding (76/76 nt) | lysY | tRNA‑Lys |
| ? | NC_000913 | 781653 = | 86 (1.080) | intergenic (+1/‑432) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | = 4606166 | 111 (1.040) | 6 (0.080) | 5/420 | 7.1 | 7.9% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 61 (0.810) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | = 2521006 | 95 (0.890) | 6 (0.080) | 5/446 | 7.4 | 8.8% | noncoding (76/76 nt) | valU | tRNA‑Val |
| ? | NC_000913 | 2521249 = | 53 (0.660) | intergenic (+1/‑4) | valY/lysV | tRNA‑Val/tRNA‑Lys | |||||
| * | ? | NC_000913 | = 2357652 | 129 (1.200) | 8 (0.080) | 6/530 | 7.9 | 7.2% | coding (749/900 nt) | rpnE | inactive recombination‑promoting nuclease‑like protein RpnE |
| ? | NC_000913 | 2357836 = | 92 (0.970) | intergenic (+33/+206) | rpnE/yfaU | inactive recombination‑promoting nuclease‑like protein RpnE/2‑keto‑3‑deoxy‑L‑rhamnonate aldolase | |||||
| * | ? | NC_000913 | = 4392437 | 80 (0.750) | 4 (0.050) | 4/442 | 8.0 | 4.8% | intergenic (+2/‑35) | glyV/glyX | tRNA‑Gly/tRNA‑Gly |
| ? | NC_000913 | 4392661 = | 98 (1.240) | intergenic (+3/‑231) | glyY/yjeV | tRNA‑Gly/uncharacterized protein YjeV | |||||
| * | ? | NC_000913 | = 1286906 | 80 (0.750) | 9 (0.090) | 6/558 | 8.2 | 11.5% | coding (198/276 nt) | ychS | putative uncharacterized protein YchS |
| ? | NC_000913 | 1287557 = | 64 (0.640) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||