mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 204 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 196,340 | 0 | A | . | 58.4% | 232.5 / inf | 582 | coding (1846/26049 nt) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 5,227,996 | 0 | C | G | 53.8% | ‑6.7 / 11.6 | 26 | R433P (CGG→CCG) | PP_4603 | transposase |
| * | NC_002947 | 4,353,698 | 0 | A | G | 50.2% | 225.5 / inf | 723 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 699,725 | 0 | A | G | 48.1% | 121.1 / inf | 595 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 4,345,074 | 0 | A | G | 47.3% | 76.6 / 221.3 | 168 | intergenic (+66/‑265) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 1,332,076 | 0 | C | T | 47.2% | 345.9 / inf | 624 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 4,345,076 | 0 | A | G | 46.9% | 77.0 / 218.4 | 165 | intergenic (+68/‑263) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,345,075 | 0 | C | T | 46.6% | 76.8 / 218.7 | 165 | intergenic (+67/‑264) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,345,077 | 0 | C | T | 46.1% | 85.1 / 219.6 | 165 | intergenic (+69/‑262) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 2,287,762 | 0 | T | G | 46.0% | 121.4 / inf | 352 | intergenic (‑162/+67) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 4,345,082 | 0 | G | C | 45.9% | 129.7 / 266.2 | 183 | intergenic (+74/‑257) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,813,174 | 0 | A | C | 44.2% | 41.5 / 157.4 | 113 | intergenic (‑289/‑266) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 4,813,175 | 0 | A | G | 44.2% | 40.8 / 139.1 | 113 | intergenic (‑290/‑265) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 2,287,771 | 0 | C | A | 43.7% | 200.4 / inf | 328 | intergenic (‑171/+58) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 4,345,069 | 0 | G | C | 43.2% | 156.5 / 244.8 | 176 | intergenic (+61/‑270) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 195,634 | 0 | C | T | 43.2% | 438.3 / inf | 742 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 4,345,083 | 0 | A | T | 42.7% | 152.1 / 224.0 | 182 | intergenic (+75/‑256) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,345,068 | 0 | A | T | 42.2% | 144.1 / 233.9 | 188 | intergenic (+60/‑271) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 2,287,767 | 0 | G | C | 41.5% | 261.4 / inf | 324 | intergenic (‑167/+62) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 2,287,766 | 0 | G | C | 41.0% | 271.2 / inf | 324 | intergenic (‑166/+63) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| Marginal new junction evidence (lowest skew 10 of 289 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | 4813168 = | 75 (0.180) | 248 (0.770) | 80/220 | 4.2 | 58.9% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5993940 | 289 (0.890) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 652785 | 407 (0.950) | 197 (0.540) | 69/250 | 7.7 | 52.9% | coding (1961/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947 | = 4813153 | 0 (0.000) | intergenic (‑268/‑287) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947 | = 4813173 | 63 (0.150) | 191 (0.490) | 69/266 | 8.7 | 48.0% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 5993770 = | 356 (0.910) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 4813173 | 63 (0.150) | 142 (0.390) | 50/250 | 11.9 | 40.8% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5993954 | 358 (0.970) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 1972169 | 201 (0.470) | 52 (0.160) | 29/224 | 16.7 | 25.2% | intergenic (+47/+72) | PP_1762/yciK | hypothetical protein/putative oxidoreductase |
| ? | NC_002947 | = 1972199 | 154 (0.470) | intergenic (+77/+42) | PP_1762/yciK | hypothetical protein/putative oxidoreductase | |||||
| * | ? | NC_002947 | 4901372 = | 270 (0.630) | 67 (0.180) | 32/248 | 17.3 | 22.6% | intergenic (+11/‑197) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein |
| ? | NC_002947 | 4901461 = | 229 (0.630) | intergenic (+100/‑108) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein | |||||
| * | ? | NC_002947 | 1972137 = | 208 (0.490) | 81 (0.250) | 27/224 | 17.5 | 34.3% | intergenic (+15/+104) | PP_1762/yciK | hypothetical protein/putative oxidoreductase |
| ? | NC_002947 | 1972233 = | 150 (0.460) | intergenic (+111/+8) | PP_1762/yciK | hypothetical protein/putative oxidoreductase | |||||
| * | ? | NC_002947 | 4652552 = | 157 (0.370) | 57 (0.180) | 24/212 | 17.8 | 27.1% | intergenic (+10/+121) | fusB/PP_4112 | elongation factor G 2/sulfate transporter |
| ? | NC_002947 | 4652660 = | 192 (0.620) | intergenic (+118/+13) | fusB/PP_4112 | elongation factor G 2/sulfate transporter | |||||
| * | ? | NC_002947 | 6011544 = | 202 (0.470) | 65 (0.200) | 25/218 | 17.9 | 34.5% | intergenic (+7/+92) | ydcJ/PP_5261 | metalloprotein/LysR family transcriptional regulator |
| ? | NC_002947 | 6011628 = | 95 (0.300) | intergenic (+91/+8) | ydcJ/PP_5261 | metalloprotein/LysR family transcriptional regulator | |||||
| * | ? | NC_002947 | = 1975731 | 364 (0.850) | 68 (0.180) | 30/250 | 18.2 | 17.6% | intergenic (+33/‑233) | mtnA/PP_mr25 | methylthioribose‑1‑phosphate isomerase/gyrA regulatory region |
| ? | NC_002947 | = 1975793 | 321 (0.870) | intergenic (+95/‑171) | mtnA/PP_mr25 | methylthioribose‑1‑phosphate isomerase/gyrA regulatory region | |||||