mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 62 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 4,741,273 | 1 | . | C | 69.6% | 49.7 / 21.0 | 23 | intergenic (+464/+288) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,275 | 0 | A | G | 69.6% | 27.1 / 11.4 | 23 | intergenic (+466/+286) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,298 | 1 | . | T | 52.0% | 40.5 / 42.2 | 25 | intergenic (+489/+263) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,302 | 0 | A | G | 52.0% | ‑1.4 / 28.2 | 25 | intergenic (+493/+259) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,305 | 0 | A | . | 52.0% | 32.6 / 54.0 | 25 | intergenic (+496/+256) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,299 | 0 | C | T | 48.0% | 0.2 / 26.8 | 25 | intergenic (+490/+262) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,301 | 0 | A | C | 48.0% | ‑5.4 / 34.5 | 25 | intergenic (+492/+260) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,304 | 0 | C | G | 48.0% | 3.1 / 32.1 | 25 | intergenic (+495/+257) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,348,749 | 0 | A | G | 44.9% | 22.9 / 57.1 | 49 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 195,634 | 0 | C | T | 43.1% | 8.1 / 67.5 | 59 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 699,725 | 0 | A | G | 41.8% | 20.8 / 55.6 | 55 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 195,559 | 0 | C | A | 40.0% | 16.8 / 15.4 | 20 | T355T (ACC→ACA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 197,590 | 0 | T | C | 32.6% | 53.8 / 37.2 | 49 | D1032D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 4,998,219 | 0 | G | T | 31.4% | 47.2 / 21.8 | 35 | intergenic (‑71/‑145) | PP_4405/PP_4406 | sensory box protein/hypothetical protein |
| * | NC_002947 | 4,998,220 | 0 | A | C | 31.4% | 27.2 / 28.0 | 35 | intergenic (‑72/‑144) | PP_4405/PP_4406 | sensory box protein/hypothetical protein |
| * | NC_002947 | 1,327,127 | 0 | C | T | 30.6% | 83.5 / 45.4 | 63 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 1,750,775 | 0 | C | G | 30.6% | 39.9 / 31.5 | 36 | A31G (GCC→GGC) | PP_1551 | replication protein O |
| * | NC_002947 | 4,741,274 | 0 | A | C | 30.4% | 23.6 / 13.6 | 23 | intergenic (+465/+287) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 1,978,751 | 0 | C | G | 29.6% | 36.6 / 17.4 | 27 | F45L (TTC→TTG) | cmk | cytidylate kinase |
| * | NC_002947 | 1,691,825 | 0 | C | A | 27.0% | 65.3 / 20.5 | 37 | intergenic (+50/‑121) | PP_1487/PP_1488 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Marginal new junction evidence (lowest skew 10 of 192 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | = 614300 | 37 (1.130) | 8 (0.320) | 8/204 | 1.9 | 19.0% | intergenic (‑116/+62) | dxs/ispA | 1‑deoxyxylulose‑5‑phosphate synthase/farnesyl diphosphate synthase |
| ? | NC_002947 | = 614316 | 40 (1.590) | intergenic (‑132/+46) | dxs/ispA | 1‑deoxyxylulose‑5‑phosphate synthase/farnesyl diphosphate synthase | |||||
| * | ? | NC_002947 | = 1392920 | 31 (0.950) | 6 (0.250) | 6/192 | 2.3 | 17.3% | intergenic (+84/‑102) | PP_1214/ruvC | transcriptional regulator/crossover junction endodeoxyribonuclease RuvC |
| ? | NC_002947 | = 1392946 | 35 (1.480) | intergenic (+110/‑76) | PP_1214/ruvC | transcriptional regulator/crossover junction endodeoxyribonuclease RuvC | |||||
| * | ? | NC_002947 | 90359 = | 60 (1.830) | 9 (0.310) | 8/234 | 2.3 | 15.6% | intergenic (+34/+88) | PP_0079/PP_0080 | transcriptional regulator/hypothetical protein |
| ? | NC_002947 | 90414 = | 45 (1.560) | intergenic (+89/+33) | PP_0079/PP_0080 | transcriptional regulator/hypothetical protein | |||||
| * | ? | NC_002947 | 4700790 = | 42 (1.280) | 7 (0.240) | 7/238 | 2.6 | 15.5% | intergenic (‑57/+93) | kdpD/kdpC | sensor protein/potassium‑transporting ATPase subunit C |
| ? | NC_002947 | 4700862 = | 39 (1.330) | intergenic (‑129/+21) | kdpD/kdpC | sensor protein/potassium‑transporting ATPase subunit C | |||||
| * | ? | NC_002947 | 2045058 = | 33 (1.010) | 8 (0.250) | 8/264 | 2.6 | 19.3% | coding (229/1941 nt) | PP_1819 | methyl‑accepting chemotaxis transducer |
| ? | NC_002947 | 2045091 = | 34 (1.040) | coding (262/1941 nt) | PP_1819 | methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947 | 1799893 = | 50 (1.520) | 6 (0.220) | 6/220 | 2.6 | 15.7% | intergenic (+21/‑166) | rnhB/dnaEA | ribonuclease HII/DNA polymerase III subunit alpha |
| ? | NC_002947 | 1799981 = | 23 (0.850) | intergenic (+109/‑78) | rnhB/dnaEA | ribonuclease HII/DNA polymerase III subunit alpha | |||||
| * | ? | NC_002947 | = 610847 | 43 (1.310) | 2 (0.090) +47 bp |
4/172 | 2.6 | 8.0% | coding (2/1926 nt) | PP_0525 | B12 family TonB‑dependent receptor |
| ? | NC_002947 | = 2233307 | 28 (0.850) | intergenic (+224/+7) | PP_1971/PP_t63 | hypothetical protein/tRNA‑Asn | |||||
| * | ? | NC_002947 | = 4896443 | 44 (1.340) | 9 (0.330) | 6/224 | 2.7 | 18.6% | intergenic (+31/‑177) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein |
| ? | NC_002947 | = 4896490 | 42 (1.520) | intergenic (+78/‑130) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein | |||||
| * | ? | NC_002947 | = 4583538 | 38 (1.160) | 6 (0.220) | 6/226 | 2.7 | 14.2% | intergenic (‑67/+104) | treSB/glgE | bifunctional trehalose synthase B/maltokinase/alpha‑1,4‑glucan:maltose‑1‑phosphate maltosyltransferase |
| ? | NC_002947 | = 4583599 | 40 (1.440) | intergenic (‑128/+43) | treSB/glgE | bifunctional trehalose synthase B/maltokinase/alpha‑1,4‑glucan:maltose‑1‑phosphate maltosyltransferase | |||||
| * | ? | NC_002947 | = 6087618 | 39 (1.190) | 8 (0.250) | 7/256 | 2.8 | 16.9% | intergenic (+13/‑217) | oruR/aphA | ornithine utilization transcriptional regulator/acetylpolyamine aminohydrolase |
| ? | NC_002947 | = 6087702 | 41 (1.300) | intergenic (+97/‑133) | oruR/aphA | ornithine utilization transcriptional regulator/acetylpolyamine aminohydrolase | |||||