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 168 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 70,289 | 0 | G | T | 54.1% | 42.1 / inf | 280 | intergenic (‑241/‑98) | araB/araC | ribulokinase/DNA‑binding transcriptional dual regulator AraC |
| * | NC_000913 | 70,371 | 0 | T | C | 53.2% | 51.8 / inf | 311 | intergenic (‑323/‑16) | araB/araC | ribulokinase/DNA‑binding transcriptional dual regulator AraC |
| * | NC_000913 | 581,322 | 0 | C | T | 52.0% | 71.3 / 312.1 | 207 | A163A (GCC→GCT) | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,337 | 0 | G | A | 51.4% | 71.6 / inf | 216 | L168L (CTG→CTA) ‡ | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,335 | 0 | C | A | 51.2% | 2.3 / inf | 215 | L168M (CTG→ATG) ‡ | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 70,434 | 0 | C | T | 50.7% | 54.8 / inf | 305 | N16N (AAC→AAT) | araC | DNA‑binding transcriptional dual regulator AraC |
| * | NC_000913 | 581,381 | 0 | A | G | 49.3% | 16.6 / inf | 216 | intergenic (+2/‑153) | nohD/tfaD | putative DNA‑packaging protein NohD/putative tail fiber assembly protein TfaD |
| * | NC_000913 | 581,380 | 0 | C | G | 49.1% | 21.1 / inf | 216 | intergenic (+1/‑154) | nohD/tfaD | putative DNA‑packaging protein NohD/putative tail fiber assembly protein TfaD |
| * | NC_000913 | 71,079 | 0 | C | T | 49.0% | 4.5 / inf | 243 | R231R (CGC→CGT) | araC | DNA‑binding transcriptional dual regulator AraC |
| * | NC_000913 | 70,740 | 0 | T | G | 48.3% | 3.7 / inf | 201 | G118G (GGT→GGG) | araC | DNA‑binding transcriptional dual regulator AraC |
| * | NC_000913 | 71,082 | 0 | T | C | 48.2% | 35.0 / inf | 245 | I232I (ATT→ATC) | araC | DNA‑binding transcriptional dual regulator AraC |
| * | NC_000913 | 71,175 | 0 | A | G | 48.0% | 39.0 / inf | 271 | R263R (CGA→CGG) | araC | DNA‑binding transcriptional dual regulator AraC |
| * | NC_000913 | 71,109 | 0 | T | C | 47.8% | 44.5 / inf | 247 | T241T (ACT→ACC) | araC | DNA‑binding transcriptional dual regulator AraC |
| * | NC_000913 | 70,581 | 0 | C | T | 47.8% | 13.4 / inf | 245 | V65V (GTC→GTT) | araC | DNA‑binding transcriptional dual regulator AraC |
| * | NC_000913 | 71,085 | 0 | T | C | 47.8% | 33.0 / inf | 247 | S233S (AGT→AGC) | araC | DNA‑binding transcriptional dual regulator AraC |
| * | NC_000913 | 71,214 | 0 | T | C | 47.0% | 89.9 / inf | 285 | F276F (TTT→TTC) | araC | DNA‑binding transcriptional dual regulator AraC |
| * | NC_000913 | 581,443 | 0 | C | G | 46.6% | 33.1 / 295.8 | 180 | intergenic (+64/‑91) | nohD/tfaD | putative DNA‑packaging protein NohD/putative tail fiber assembly protein TfaD |
| * | NC_000913 | 581,437 | 0 | G | A | 46.2% | 37.0 / 279.8 | 182 | intergenic (+58/‑97) | nohD/tfaD | putative DNA‑packaging protein NohD/putative tail fiber assembly protein TfaD |
| * | NC_000913 | 581,455 | 0 | G | A | 46.1% | 20.8 / 284.1 | 180 | intergenic (+76/‑79) | nohD/tfaD | putative DNA‑packaging protein NohD/putative tail fiber assembly protein TfaD |
| * | NC_000913 | 581,458 | 0 | T | C | 46.1% | 53.5 / 268.0 | 180 | intergenic (+79/‑76) | nohD/tfaD | putative DNA‑packaging protein NohD/putative tail fiber assembly protein TfaD |
| Marginal new junction evidence (lowest skew 10 of 48 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 79 (0.610) | 41 (0.340) | 29/550 | 3.1 | 29.6% | coding (290/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | 1209619 = | 120 (0.980) | intergenic (‑500/‑66) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 4606166 | 135 (1.040) | 14 (0.160) | 13/404 | 4.7 | 14.1% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 77 (0.860) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | = 781222 | 110 (0.850) | 17 (0.180) | 12/430 | 5.4 | 17.0% | noncoding (76/76 nt) | lysY | tRNA‑Lys |
| ? | NC_000913 | 781445 = | 85 (0.890) | intergenic (+1/‑132) | lysZ/lysQ | tRNA‑Lys/tRNA‑Lys | |||||
| * | ? | NC_000913 | = 696741 | 95 (0.730) | 12 (0.130) | 11/426 | 5.7 | 13.8% | intergenic (‑1/+15) | metU/glnW | tRNA‑Met/tRNA‑Gln |
| ? | NC_000913 | 697135 = | 81 (0.860) | intergenic (‑2/+378) | metT/asnB | tRNA‑Met/asparagine synthetase B | |||||
| * | ? | NC_000913 | = 2653419 | 128 (0.990) | 13 (0.110) | 12/532 | 6.7 | 9.3% | noncoding (37/100 nt) | timR | putative small regulatory RNA TimR |
| ? | NC_000913 | 2653746 = | 138 (1.170) | intergenic (‑291/‑109) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA | |||||
| * | ? | NC_000913 | = 4542690 | 161 (1.240) | 13 (0.100) | 11/564 | 7.4 | 7.7% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 156 (1.240) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 3648146 | 143 (1.100) | 10 (0.100) | 8/466 | 7.4 | 8.1% | intergenic (+2/‑148) | agrA/agrB | small RNA AgrA/small regulatory RNA AgrB |
| ? | NC_000913 | 3648378 = | 114 (1.100) | intergenic (+3/‑150) | agrB/arsR | small regulatory RNA AgrB/DNA‑binding transcriptional repressor ArsR | |||||
| * | ? | NC_000913 | = 4094350 | 92 (0.710) | 11 (0.100) | 8/500 | 7.8 | 12.0% | intergenic (‑78/+373) | rhaD/rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase |
| ? | NC_000913 | 4094719 = | 82 (0.740) | intergenic (‑447/+4) | rhaD/rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase | |||||
| * | ? | NC_000913 | = 1286906 | 107 (0.830) | 9 (0.070) | 9/542 | 7.9 | 9.2% | coding (198/276 nt) | ychS | putative uncharacterized protein YchS |
| ? | NC_000913 | 1287557 = | 79 (0.660) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | 781369 = | 105 (0.810) | 10 (0.080) +G |
10/580 | 7.9 | 10.1% | noncoding (1/76 nt) | lysZ | tRNA‑Lys |
| ? | NC_000913 | = 2521128 | 73 (0.560) | intergenic (+2/‑45) | valX/valY | tRNA‑Val/tRNA‑Val | |||||