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 253 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 1,634,404 | 0 | A | G | 62.5% | 1.1 / 36.1 | 40 | I161T (ATC→ACC) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 579,134 | 0 | T | C | 62.4% | 202.6 / 299.5 | 247 | intergenic (‑241/+50) | borD/ybcV | prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 1,634,484 | 0 | G | T | 62.3% | 5.1 / 129.9 | 106 | N134K (AAC→AAA) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,482 | 0 | T | C | 61.9% | 3.8 / 120.8 | 106 | N135S (AAC→AGC) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 578,605 | 0 | T | G | 61.7% | 226.2 / 307.6 | 256 | K97Q (AAA→CAA) | borD | prophage lipoprotein BorD |
| * | NC_000913 | 578,571 | 0 | C | T | 61.3% | 224.0 / 293.0 | 248 | intergenic (+3/+29) | rzpD/borD | putative prophage endopeptidase RzpD/prophage lipoprotein BorD |
| * | NC_000913 | 579,146 | 0 | A | G | 61.2% | 202.5 / inf | 269 | intergenic (‑253/+38) | borD/ybcV | prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 578,574 | 0 | A | C | 60.9% | 231.0 / 263.0 | 248 | intergenic (+6/+26) | rzpD/borD | putative prophage endopeptidase RzpD/prophage lipoprotein BorD |
| * | NC_000913 | 578,729 | 0 | A | G | 60.6% | 169.3 / 303.6 | 257 | A55A (GCT→GCC) | borD | prophage lipoprotein BorD |
| * | NC_000913 | 578,809 | 0 | T | C | 60.5% | 164.8 / inf | 253 | T29A (ACA→GCA) | borD | prophage lipoprotein BorD |
| * | NC_000913 | 578,811 | 0 | T | G | 60.2% | 191.3 / 305.2 | 254 | Q28P (CAG→CCG) | borD | prophage lipoprotein BorD |
| * | NC_000913 | 579,127 | 0 | T | C | 59.9% | 180.5 / inf | 252 | intergenic (‑234/+57) | borD/ybcV | prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 1,634,388 | 0 | T | G | 59.5% | ‑2.6 / 37.0 | 37 | A166A (GCA→GCC) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 578,831 | 0 | T | C | 59.2% | 172.7 / inf | 288 | T21T (ACA→ACG) | borD | prophage lipoprotein BorD |
| * | NC_000913 | 579,004 | 0 | C | T | 58.9% | 224.3 / inf | 300 | intergenic (‑111/+180) | borD/ybcV | prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 1,634,597 | 0 | C | A | 58.9% | ‑3.2 / 225.7 | 175 | V97F (GTT→TTT) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 579,099 | 0 | A | . | 58.7% | 116.3 / inf | 284 | intergenic (‑206/+85) | borD/ybcV | prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 580,020 | 0 | G | A | 58.5% | 170.5 / 312.6 | 242 | R47R (AGG→AGA) | ybcW | uncharacterized protein YbcW |
| * | NC_000913 | 1,634,382 | 0 | T | C | 58.3% | ‑5.5 / 38.7 | 36 | K168K (AAA→AAG) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,578 | 0 | T | C | 58.3% | 3.7 / 229.2 | 168 | E103G (GAA→GGA) | tfaQ | putative tail fiber assembly protein TfaQ |
| Marginal new junction evidence (lowest skew 10 of 46 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 566774 | 87 (0.960) | 49 (0.540) | 21/594 | 3.0 | 34.5% | pseudogene (91/93 nt) | renD | protein RenD |
| ? | NC_000913 | 568036 = | 100 (1.110) | pseudogene (2/213 nt) | renD | protein RenD | |||||
| * | ? | NC_000913 | = 3131340 | NA (NA) | 25 (0.280) | 20/598 | 3.2 | 25.0% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 3136822 = | 75 (0.830) | coding (1701/1860 nt) | gss | fused glutathionylspermidine amidase/glutathionylspermidine synthetase | |||||
| * | ? | NC_000913 | = 2290113 | NA (NA) | 22 (0.240) | 20/598 | 3.2 | 19.3% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3658974 | 92 (1.010) | intergenic (+81/‑18) | gadE/gadF | DNA‑binding transcriptional activator GadE/small regulatory RNA GadF | |||||
| * | ? | NC_000913 | = 1388303 | 54 (0.590) | 18 (0.200) | 17/598 | 3.7 | 25.0% | intergenic (+42/+2) | tyrR/tpx | DNA‑binding transcriptional dual regulator TyrR/lipid hydroperoxide peroxidase |
| ? | NC_000913 | = 2290113 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 2288919 = | NA (NA) | 18 (0.200) | 16/598 | 4.0 | 16.4% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 3658971 = | 92 (1.010) | intergenic (+78/‑21) | gadE/gadF | DNA‑binding transcriptional activator GadE/small regulatory RNA GadF | |||||
| * | ? | NC_000913 | 1097323 = | 45 (0.500) | 11 (0.190) +112 bp |
8/374 | 4.0 | 28.1% | intergenic (+494/+242) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| ? | NC_000913 | 4498180 = | NA (NA) | intergenic (+1691/‑92) | leuX/insC6 | tRNA‑Leu/IS2 insertion element repressor InsA | |||||
| * | ? | NC_000913 | = 696741 | 67 (0.740) | 10 (0.150) | 10/442 | 4.1 | 13.7% | intergenic (‑1/+15) | metU/glnW | tRNA‑Met/tRNA‑Gln |
| ? | NC_000913 | 697135 = | 76 (1.130) | intergenic (‑2/+378) | metT/asnB | tRNA‑Met/asparagine synthetase B | |||||
| * | ? | NC_000913 | = 2171428 | NA (NA) | 15 (0.170) | 15/598 | 4.2 | 19.7% | noncoding (1258/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | 2174007 = | 61 (0.670) | intergenic (‑1134/+275) | gatD/gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component | |||||
| * | ? | NC_000913 | 1096848 = | 126 (1.390) | 20 (0.220) | 15/596 | 4.2 | 13.7% | intergenic (+19/+717) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| ? | NC_000913 | = 1469240 | NA (NA) | noncoding (1/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 2290113 | NA (NA) | 14 (0.150) | 13/598 | 4.6 | 11.6% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3262487 | 107 (1.180) | coding (1174/1209 nt) | tdcD | propionate kinase | |||||