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 144 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 581,335 | 0 | C | A | 62.9% | 159.4 / 257.1 | 222 | L168M (CTG→ATG) ‡ | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,322 | 0 | C | T | 62.6% | 260.9 / 224.6 | 214 | A163A (GCC→GCT) | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,337 | 0 | G | A | 62.3% | 252.7 / 244.2 | 223 | L168L (CTG→CTA) ‡ | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,381 | 0 | A | G | 60.5% | 153.4 / 269.3 | 211 | intergenic (+2/‑153) | nohD/tfaD | putative DNA‑packaging protein NohD/putative tail fiber assembly protein TfaD |
| * | NC_000913 | 581,380 | 0 | C | G | 59.7% | 139.3 / 293.2 | 212 | intergenic (+1/‑154) | nohD/tfaD | putative DNA‑packaging protein NohD/putative tail fiber assembly protein TfaD |
| * | NC_000913 | 581,291 | 0 | G | A | 56.6% | 95.0 / 196.7 | 168 | R153Q (CGG→CAG) ‡ | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,275 | 0 | G | A | 56.3% | 127.4 / 224.7 | 167 | V148I (GTT→ATT) | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,289 | 0 | A | G | 55.5% | 62.9 / 229.5 | 166 | K152K (AAA→AAG) | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,290 | 0 | C | A | 55.4% | 50.2 / 231.3 | 167 | R153R (CGG→AGG) ‡ | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,295 | 0 | T | C | 55.3% | 87.5 / 252.0 | 170 | D154D (GAT→GAC) | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,301 | 0 | C | T | 55.0% | 103.9 / 229.0 | 169 | I156I (ATC→ATT) | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,286 | 0 | G | C | 54.9% | 92.6 / 243.0 | 166 | L151L (CTG→CTC) | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,250 | 0 | T | C | 54.7% | 73.7 / 223.7 | 148 | R139R (CGT→CGC) | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,259 | 0 | A | G | 54.7% | 81.6 / 211.4 | 151 | E142E (GAA→GAG) | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,253 | 0 | T | C | 54.4% | 31.9 / 221.4 | 148 | F140F (TTT→TTC) | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,404 | 0 | C | G | 53.5% | 45.0 / 288.4 | 174 | intergenic (+25/‑130) | nohD/tfaD | putative DNA‑packaging protein NohD/putative tail fiber assembly protein TfaD |
| * | NC_000913 | 581,394 | 0 | T | C | 53.2% | 20.7 / 272.3 | 173 | intergenic (+15/‑140) | nohD/tfaD | putative DNA‑packaging protein NohD/putative tail fiber assembly protein TfaD |
| * | NC_000913 | 581,412 | 0 | G | T | 53.2% | 4.8 / 268.0 | 174 | intergenic (+33/‑122) | nohD/tfaD | putative DNA‑packaging protein NohD/putative tail fiber assembly protein TfaD |
| * | NC_000913 | 581,413 | 0 | C | T | 53.2% | 52.2 / 258.0 | 174 | intergenic (+34/‑121) | nohD/tfaD | putative DNA‑packaging protein NohD/putative tail fiber assembly protein TfaD |
| * | NC_000913 | 581,416 | 0 | A | G | 53.2% | 24.6 / 268.0 | 173 | intergenic (+37/‑118) | nohD/tfaD | putative DNA‑packaging protein NohD/putative tail fiber assembly protein TfaD |
| Marginal new junction evidence (lowest skew 10 of 35 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 4542682 = | 147 (1.560) | 10 (0.110) | 8/566 | 6.3 | 7.2% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 117 (1.280) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 1207800 = | 33 (0.350) | 8 (0.080) +A |
8/582 | 6.4 | 17.2% | coding (300/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | 1209610 = | 44 (0.470) | intergenic (‑491/‑75) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | 781369 = | 86 (0.910) | 13 (0.140) +G |
8/582 | 6.4 | 16.1% | noncoding (1/76 nt) | lysZ | tRNA‑Lys |
| ? | NC_000913 | = 2521127 | 50 (0.530) | intergenic (+1/‑46) | valX/valY | tRNA‑Val/tRNA‑Val | |||||
| * | ? | NC_000913 | 781369 = | 86 (0.910) | 13 (0.140) +GG |
8/580 | 6.4 | 14.5% | noncoding (1/76 nt) | lysZ | tRNA‑Lys |
| ? | NC_000913 | = 2521006 | 68 (0.720) | noncoding (76/76 nt) | valU | tRNA‑Val | |||||
| * | ? | NC_000913 | = 696506 | 70 (0.740) | 6 (0.080) +45 bp |
6/494 | 6.4 | 8.3% | intergenic (‑2/+36) | glnX/glnV | tRNA‑Gln/tRNA‑Gln |
| ? | NC_000913 | 697057 = | 86 (0.910) | noncoding (77/77 nt) | metT | tRNA‑Met | |||||
| * | ? | NC_000913 | = 696454 | 75 (0.790) | 10 (0.110) | 7/562 | 6.6 | 12.7% | noncoding (51/75 nt) | glnX | tRNA‑Gln |
| ? | NC_000913 | 696890 = | 65 (0.710) | noncoding (50/75 nt) | glnU | tRNA‑Gln | |||||
| * | ? | NC_000913 | 3270072 = | 61 (0.650) | 5 (0.060) +25 bp |
5/534 | 7.3 | 6.6% | intergenic (+470/+144) | yhaC/rnpB | uncharacterized protein YhaC/RNase P catalytic RNA component |
| ? | NC_000913 | 4137788 = | 94 (0.990) | intergenic (‑131/+144) | yijF/gldA | DUF1287 domain‑containing protein YijF/L‑1,2‑propanediol dehydrogenase/glycerol dehydrogenase | |||||
| * | ? | NC_000913 | = 2653389 | 105 (1.110) | 5 (0.050) | 5/574 | 7.7 | 4.8% | noncoding (67/100 nt) | timR | putative small regulatory RNA TimR |
| ? | NC_000913 | 2653716 = | 94 (1.010) | intergenic (‑261/‑139) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA | |||||
| * | ? | NC_000913 | = 1286892 | 75 (0.790) | 5 (0.050) +C |
5/582 | 7.7 | 6.3% | coding (184/276 nt) | ychS | putative uncharacterized protein YchS |
| ? | NC_000913 | 1287544 = | 75 (0.790) | noncoding (79/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 780918 | 70 (0.740) | 6 (0.070) | 4/548 | 7.9 | 7.8% | noncoding (76/76 nt) | lysW | tRNA‑Lys |
| ? | NC_000913 | 781321 = | 76 (0.860) | intergenic (+99/‑48) | lysY/lysZ | tRNA‑Lys/tRNA‑Lys | |||||