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 245 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 579,099 | 0 | A | . | 53.8% | inf / inf | 288 | intergenic (‑206/+85) | borD/ybcV | prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 1,634,724 | 0 | G | A | 52.6% | 46.3 / 222.3 | 154 | F54F (TTC→TTT) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 579,004 | 0 | C | T | 52.3% | 65.2 / inf | 298 | intergenic (‑111/+180) | borD/ybcV | prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 579,134 | 0 | T | C | 51.9% | 2.8 / inf | 264 | intergenic (‑241/+50) | borD/ybcV | prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 579,271 | 0 | G | A | 51.1% | 46.7 / inf | 308 | H108H (CAC→CAT) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 579,146 | 0 | A | G | 51.1% | ‑6.4 / inf | 276 | intergenic (‑253/+38) | borD/ybcV | prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 4,542,682 | 0 | T | . | 51.1% | inf / inf | 327 | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| * | NC_000913 | 1,634,699 | 0 | A | C | 50.9% | 60.3 / 258.9 | 173 | S63A (TCA→GCA) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 579,127 | 0 | T | C | 50.7% | ‑5.1 / inf | 267 | intergenic (‑234/+57) | borD/ybcV | prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 579,285 | 0 | T | C | 50.0% | 50.1 / inf | 312 | I104V (ATT→GTT) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 1,634,676 | 0 | A | G | 49.7% | 79.6 / 297.0 | 181 | D70D (GAT→GAC) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 578,605 | 0 | T | G | 49.6% | 39.5 / inf | 254 | K97Q (AAA→CAA) | borD | prophage lipoprotein BorD |
| * | NC_000913 | 578,831 | 0 | T | C | 49.5% | 29.7 / inf | 280 | T21T (ACA→ACG) | borD | prophage lipoprotein BorD |
| * | NC_000913 | 579,457 | 0 | A | G | 48.9% | 64.7 / inf | 352 | I46I (ATT→ATC) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 578,574 | 0 | A | C | 48.8% | 14.1 / inf | 252 | intergenic (+6/+26) | rzpD/borD | putative prophage endopeptidase RzpD/prophage lipoprotein BorD |
| * | NC_000913 | 580,302 | 0 | C | T | 48.6% | 23.7 / inf | 258 | R48R (AGG→AGA) | ylcI | DUF3950 domain‑containing protein YlcI |
| * | NC_000913 | 578,571 | 0 | C | T | 48.4% | ‑2.3 / inf | 252 | intergenic (+3/+29) | rzpD/borD | putative prophage endopeptidase RzpD/prophage lipoprotein BorD |
| * | NC_000913 | 578,729 | 0 | A | G | 48.4% | 14.2 / inf | 247 | A55A (GCT→GCC) | borD | prophage lipoprotein BorD |
| * | NC_000913 | 579,811 | 0 | C | T | 48.4% | 8.7 / inf | 274 | intergenic (‑217/‑69) | ybcV/ybcW | DUF1398 domain‑containing protein YbcV/uncharacterized protein YbcW |
| * | NC_000913 | 579,717 | 0 | A | C | 48.3% | ‑2.3 / inf | 354 | intergenic (‑123/‑163) | ybcV/ybcW | DUF1398 domain‑containing protein YbcV/uncharacterized protein YbcW |
| 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 | 382179 = | NA (NA) | 31 (0.290) | 22/594 | 3.9 | NA | noncoding (920/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 382590 | NA (NA) | noncoding (1331/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 566774 | 167 (1.540) | 44 (0.410) | 17/594 | 5.0 | 19.9% | pseudogene (91/93 nt) | renD | protein RenD |
| ? | NC_000913 | 568036 = | 188 (1.740) | pseudogene (2/213 nt) | renD | protein RenD | |||||
| * | ? | NC_000913 | = 3648146 | 120 (1.100) | 8 (0.090) | 8/482 | 6.6 | 7.9% | intergenic (+2/‑148) | agrA/agrB | small RNA AgrA/small regulatory RNA AgrB |
| ? | NC_000913 | 3648378 = | 90 (1.030) | intergenic (+3/‑150) | agrB/arsR | small regulatory RNA AgrB/DNA‑binding transcriptional repressor ArsR | |||||
| * | ? | NC_000913 | = 696741 | 74 (0.680) | 8 (0.100) | 6/442 | 7.0 | 12.3% | intergenic (‑1/+15) | metU/glnW | tRNA‑Met/tRNA‑Gln |
| ? | NC_000913 | 697135 = | 59 (0.730) | intergenic (‑2/+378) | metT/asnB | tRNA‑Met/asparagine synthetase B | |||||
| * | ? | NC_000913 | 1411899 = | 140 (1.290) | 7 (0.070) | 7/546 | 7.7 | 5.0% | coding (50/936 nt) | ttcA | tRNA cytosine(32) 2‑sulfurtransferase TtcA |
| ? | NC_000913 | = 1434958 | 141 (1.420) | intergenic (‑552/+227) | ynaM/uspF | protein YnaM/universal stress protein F | |||||
| * | ? | NC_000913 | = 1287123 | 78 (0.720) | 8 (0.080) | 7/580 | 8.1 | 9.4% | noncoding (114/171 nt) coding (54/90 nt) |
rttR tpr |
small RNA RttR protamine‑like protein |
| ? | NC_000913 | 1287421 = | 79 (0.750) | intergenic (‑93/+117) | tyrV/tyrT | tRNA‑Tyr/tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 2653419 | 92 (0.850) | 6 (0.060) | 6/548 | 8.2 | 6.3% | noncoding (37/100 nt) | timR | putative small regulatory RNA TimR |
| ? | NC_000913 | 2653746 = | 95 (0.950) | intergenic (‑291/‑109) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA | |||||
| * | ? | NC_000913 | = 1286945 | 52 (0.480) | 7 (0.070) | 6/580 | 8.6 | 9.8% | coding (237/276 nt) | ychS | putative uncharacterized protein YchS |
| ? | NC_000913 | 1287421 = | 79 (0.750) | intergenic (‑93/+117) | tyrV/tyrT | tRNA‑Tyr/tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 781446 | 62 (0.570) | 3 (0.040) | 3/442 | 8.7 | 5.3% | intergenic (+2/‑131) | lysZ/lysQ | tRNA‑Lys/tRNA‑Lys |
| ? | NC_000913 | 781655 = | 62 (0.770) | intergenic (+3/‑430) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | = 1376615 | 80 (0.740) | 5 (0.050) | 5/572 | 9.0 | 6.0% | coding (582/789 nt) | ycjR | 3‑dehydro‑D‑guloside 4‑epimerase |
| ? | NC_000913 | 1376985 = | 80 (0.770) | coding (154/1056 nt) | ycjS | D‑glucoside 3‑dehydrogenase | |||||