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 196 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 | . | 57.1% | 179.8 / inf | 533 | coding (1846/26049 nt) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 1,332,076 | 0 | C | T | 50.8% | 218.4 / inf | 566 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 5,227,996 | 0 | C | G | 50.0% | ‑6.2 / 11.8 | 14 | R433P (CGG→CCG) | PP_4603 | transposase |
| * | NC_002947 | 4,353,698 | 0 | A | G | 48.4% | 259.0 / inf | 591 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 699,725 | 0 | A | G | 48.4% | 95.1 / inf | 425 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 4,345,077 | 0 | C | T | 46.5% | 79.9 / 218.9 | 163 | intergenic (+69/‑262) | 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 | 46.0% | 86.6 / 215.1 | 163 | intergenic (+67/‑264) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,345,082 | 0 | G | C | 45.6% | 130.0 / 250.7 | 170 | intergenic (+74/‑257) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,345,074 | 0 | A | G | 45.5% | 102.2 / 212.1 | 167 | intergenic (+66/‑265) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,345,076 | 0 | A | G | 45.1% | 102.7 / 206.2 | 163 | intergenic (+68/‑263) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 3,822,630 | 0 | C | G | 43.8% | 22.6 / 40.9 | 32 | F207L (TTC→TTG) | bamA‑II | outer membrane protein assembly factor |
| * | NC_002947 | 4,345,068 | 0 | A | T | 43.7% | 123.1 / 229.8 | 180 | intergenic (+60/‑271) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,345,069 | 0 | G | C | 43.6% | 147.9 / 243.4 | 173 | intergenic (+61/‑270) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,345,083 | 0 | A | T | 43.5% | 135.7 / 222.8 | 171 | intergenic (+75/‑256) | 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 | 42.7% | 192.9 / inf | 331 | intergenic (‑162/+67) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 2,287,771 | 0 | C | A | 42.4% | 204.0 / inf | 316 | intergenic (‑171/+58) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 1,018,200 | 0 | A | T | 41.3% | 215.2 / inf | 287 | intergenic (+76/+55) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947 | 1,018,201 | 0 | T | G | 41.2% | 218.8 / inf | 276 | intergenic (+77/+54) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947 | 5,745,472 | 0 | T | G | 40.8% | 148.8 / 272.0 | 228 | intergenic (+32/+39) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947 | 2,287,767 | 0 | G | C | 40.1% | 257.5 / inf | 306 | intergenic (‑167/+62) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| Marginal new junction evidence (lowest skew 10 of 364 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | 4813168 = | 53 (0.150) | 191 (0.710) | 72/216 | 3.6 | 58.9% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5993940 | 227 (0.840) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 652785 | 394 (1.100) | 144 (0.470) | 66/246 | 5.8 | 46.0% | 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 | 57 (0.160) | 203 (0.620) | 65/262 | 6.7 | 53.9% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 5993770 = | 295 (0.900) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 4813173 | 57 (0.160) | 193 (0.630) | 48/246 | 9.1 | 54.4% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5993954 | 275 (0.900) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 1975731 | 298 (0.830) | 78 (0.250) | 38/246 | 11.5 | 23.1% | intergenic (+33/‑233) | mtnA/PP_mr25 | methylthioribose‑1‑phosphate isomerase/gyrA regulatory region |
| ? | NC_002947 | = 1975793 | 263 (0.860) | intergenic (+95/‑171) | mtnA/PP_mr25 | methylthioribose‑1‑phosphate isomerase/gyrA regulatory region | |||||
| * | ? | NC_002947 | 6014114 = | 162 (0.450) | 72 (0.260) | 30/220 | 12.3 | 43.2% | intergenic (+6/+76) | norM/PP_5263 | multidrug resistance protein NorM/GGDEF domain‑containing protein |
| ? | NC_002947 | 6014191 = | 65 (0.240) | coding (1667/1668 nt) | PP_5263 | GGDEF domain‑containing protein | |||||
| * | ? | NC_002947 | = 4901392 | 219 (0.610) | 79 (0.260) | 34/244 | 12.5 | 28.0% | intergenic (+31/‑177) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein |
| ? | NC_002947 | = 4901439 | 220 (0.720) | intergenic (+78/‑130) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein | |||||
| * | ? | NC_002947 | = 2055587 | 212 (0.590) | 50 (0.190) | 27/212 | 12.8 | 25.7% | intergenic (‑88/+87) | PP_1824/PP_1825 | Smr domain‑containing protein/hypothetical protein |
| ? | NC_002947 | = 2055623 | 133 (0.500) | intergenic (‑124/+51) | PP_1824/PP_1825 | Smr domain‑containing protein/hypothetical protein | |||||
| * | ? | NC_002947 | = 5482127 | 124 (0.350) | 57 (0.220) | 25/204 | 13.0 | 38.6% | intergenic (+43/+69) | PP_4813/PP_4814 | PAP2 family protein/DedA family protein/ATP‑dependent protease La domain‑containing protein |
| ? | NC_002947 | = 5482144 | 93 (0.370) | intergenic (+60/+52) | PP_4813/PP_4814 | PAP2 family protein/DedA family protein/ATP‑dependent protease La domain‑containing protein | |||||
| * | ? | NC_002947 | 1491962 = | 239 (0.670) | 68 (0.240) | 28/226 | 13.3 | 28.3% | intergenic (+22/+108) | yhdZ/degS | amino acid ABC transporter ATP‑binding protein/serine endoprotease DegS |
| ? | NC_002947 | 1492052 = | 156 (0.550) | intergenic (+112/+18) | yhdZ/degS | amino acid ABC transporter ATP‑binding protein/serine endoprotease DegS | |||||