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 255 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 | 56.2% | 125.3 / inf | 233 | intergenic (+29/+136) | ybcW/ylcI | uncharacterized protein YbcW/DUF3950 domain‑containing protein YlcI |
| * | NC_000913 | 578,605 | 0 | T | G | 55.6% | 117.8 / inf | 259 | K97Q (AAA→CAA) | borD | prophage lipoprotein BorD |
| * | NC_000913 | 580,120 | 0 | C | T | 55.0% | 106.7 / inf | 231 | intergenic (+34/+131) | ybcW/ylcI | uncharacterized protein YbcW/DUF3950 domain‑containing protein YlcI |
| * | NC_000913 | 580,119 | 0 | A | G | 54.8% | 73.8 / inf | 230 | intergenic (+33/+132) | ybcW/ylcI | uncharacterized protein YbcW/DUF3950 domain‑containing protein YlcI |
| * | NC_000913 | 580,020 | 0 | G | A | 54.1% | 105.7 / inf | 258 | R47R (AGG→AGA) | ybcW | uncharacterized protein YbcW |
| * | NC_000913 | 578,574 | 0 | A | C | 53.6% | 107.5 / inf | 253 | intergenic (+6/+26) | rzpD/borD | putative prophage endopeptidase RzpD/prophage lipoprotein BorD |
| * | NC_000913 | 578,571 | 0 | C | T | 53.4% | 70.0 / inf | 253 | intergenic (+3/+29) | rzpD/borD | putative prophage endopeptidase RzpD/prophage lipoprotein BorD |
| * | NC_000913 | 578,811 | 0 | T | G | 52.6% | 79.0 / inf | 249 | Q28P (CAG→CCG) | borD | prophage lipoprotein BorD |
| * | NC_000913 | 579,811 | 0 | C | T | 52.6% | 70.0 / inf | 268 | intergenic (‑217/‑69) | ybcV/ybcW | DUF1398 domain‑containing protein YbcV/uncharacterized protein YbcW |
| * | NC_000913 | 578,809 | 0 | T | C | 52.2% | 19.9 / inf | 250 | T29A (ACA→GCA) | borD | prophage lipoprotein BorD |
| * | NC_000913 | 578,729 | 0 | A | G | 52.1% | 11.7 / inf | 264 | A55A (GCT→GCC) | borD | prophage lipoprotein BorD |
| * | NC_000913 | 580,302 | 0 | C | T | 51.4% | 21.1 / inf | 251 | R48R (AGG→AGA) | ylcI | DUF3950 domain‑containing protein YlcI |
| * | NC_000913 | 578,831 | 0 | T | C | 50.9% | 7.9 / inf | 279 | T21T (ACA→ACG) | borD | prophage lipoprotein BorD |
| * | NC_000913 | 579,717 | 0 | A | C | 50.6% | 38.1 / inf | 346 | intergenic (‑123/‑163) | ybcV/ybcW | DUF1398 domain‑containing protein YbcV/uncharacterized protein YbcW |
| * | NC_000913 | 579,004 | 0 | C | T | 50.0% | 21.1 / inf | 286 | intergenic (‑111/+180) | borD/ybcV | prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 579,127 | 0 | T | C | 50.0% | 9.0 / inf | 226 | intergenic (‑234/+57) | borD/ybcV | prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 579,134 | 0 | T | C | 50.0% | 4.6 / inf | 222 | intergenic (‑241/+50) | borD/ybcV | prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 579,671 | 0 | T | C | 50.0% | 33.0 / inf | 331 | intergenic (‑77/‑209) | ybcV/ybcW | DUF1398 domain‑containing protein YbcV/uncharacterized protein YbcW |
| * | NC_000913 | 1,429,345 | 0 | T | G | 49.5% | 6.0 / 171.9 | 107 | R99R (CGT→CGG) | stfR | putative prophage side tail fiber protein StfR |
| * | NC_000913 | 1,429,319 | 0 | G | T | 49.1% | 20.5 / 158.5 | 109 | G91C (GGT→TGT) | stfR | putative prophage side tail fiber protein StfR |
| Marginal new junction evidence (lowest skew 10 of 20 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 566774 | 117 (1.200) | 48 (0.500) | 18/594 | 4.1 | 30.3% | pseudogene (91/93 nt) | renD | protein RenD |
| ? | NC_000913 | 568036 = | 105 (1.090) | pseudogene (2/213 nt) | renD | protein RenD | |||||
| * | ? | NC_000913 | = 4542690 | 161 (1.660) | 14 (0.150) | 13/580 | 5.2 | 8.9% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 132 (1.400) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 696741 | 54 (0.560) | 8 (0.110) | 8/442 | 5.4 | 14.8% | intergenic (‑1/+15) | metU/glnW | tRNA‑Met/tRNA‑Gln |
| ? | NC_000913 | 697135 = | 52 (0.720) | intergenic (‑2/+378) | metT/asnB | tRNA‑Met/asparagine synthetase B | |||||
| * | ? | NC_000913 | 4542682 = | 159 (1.640) | 15 (0.160) | 12/580 | 5.5 | 9.5% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 132 (1.400) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 1096961 = | 80 (0.820) | 9 (0.130) | 7/438 | 5.7 | 14.3% | intergenic (+132/+604) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| ? | NC_000913 | = 1097503 | 49 (0.690) | intergenic (+674/+62) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser | |||||
| * | ? | NC_000913 | 2818197 = | 30 (0.310) | 7 (0.120) +114 bp |
4/370 | 6.3 | 27.4% | intergenic (‑62/+1) | argZ/argY | tRNA‑Arg/tRNA‑Arg |
| ? | NC_000913 | = 2818216 | 30 (0.310) | noncoding (59/77 nt) | argY | tRNA‑Arg | |||||
| * | ? | NC_000913 | 3270072 = | 53 (0.550) | 9 (0.100) +25 bp |
8/548 | 6.5 | 11.5% | intergenic (+470/+144) | yhaC/rnpB | uncharacterized protein YhaC/RNase P catalytic RNA component |
| ? | NC_000913 | 4137788 = | 98 (1.010) | intergenic (‑131/+144) | yijF/gldA | DUF1287 domain‑containing protein YijF/L‑1,2‑propanediol dehydrogenase/glycerol dehydrogenase | |||||
| * | ? | NC_000913 | = 2357742 | 95 (0.980) | 10 (0.110) | 8/576 | 6.8 | 9.4% | coding (839/900 nt) | rpnE | inactive recombination‑promoting nuclease‑like protein RpnE |
| ? | NC_000913 | 2357938 = | 101 (1.080) | intergenic (+135/+104) | rpnE/yfaU | inactive recombination‑promoting nuclease‑like protein RpnE/2‑keto‑3‑deoxy‑L‑rhamnonate aldolase | |||||
| * | ? | NC_000913 | = 2817934 | 55 (0.570) | 8 (0.080) +T |
8/596 | 7.0 | 12.0% | intergenic (‑74/+125) | argQ/argZ | tRNA‑Arg/tRNA‑Arg |
| ? | NC_000913 | 2818485 = | 63 (0.650) | noncoding (65/77 nt) | argV | tRNA‑Arg | |||||
| * | ? | NC_000913 | = 2653389 | 88 (0.910) | 7 (0.070) | 7/588 | 7.3 | 7.8% | noncoding (67/100 nt) | timR | putative small regulatory RNA TimR |
| ? | NC_000913 | 2653716 = | 80 (0.840) | intergenic (‑261/‑139) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA | |||||