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 | 4,813,174 | 0 | A | C | 52.2% | ‑1.8 / 71.3 | 48 | 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 | 51.1% | ‑3.0 / 67.5 | 48 | intergenic (‑290/‑265) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 4,353,698 | 0 | A | G | 49.5% | 271.3 / inf | 695 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 1,332,076 | 0 | C | T | 48.8% | 243.4 / inf | 446 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 699,725 | 0 | A | G | 43.8% | 214.4 / inf | 384 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 195,634 | 0 | C | T | 38.9% | 445.1 / inf | 497 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 4,882,318 | 0 | G | C | 28.2% | 621.5 / 121.4 | 298 | intergenic (‑372/‑28) | pucM/puuE | 5‑hydroxyisourate hydrolase/allantoinase |
| * | NC_002947 | 195,559 | 0 | C | A | 27.4% | 730.7 / 264.2 | 379 | T355T (ACC→ACA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 1,549,350 | 0 | C | G | 27.3% | 625.0 / 101.6 | 315 | A388G (GCG→GGG) | mdfA | multidrug MFS transporter |
| * | NC_002947 | 2,562,908 | 0 | A | C | 26.4% | 632.0 / 50.4 | 313 | E59A (GAG→GCG) | fepA | ferric enterobactin transport system outer membrane subunit |
| * | NC_002947 | 3,471,833 | 0 | T | G | 26.4% | 700.4 / 74.7 | 400 | intergenic (‑16/+108) | PP_3081/PP_5560 | hypothetical protein/hypothetical protein |
| * | NC_002947 | 3,877,805 | 0 | T | G | 26.2% | 518.7 / 30.7 | 247 | Q443P (CAG→CCG) | PP_3421 | sensor histidine kinase |
| * | NC_002947 | 1,798,394 | 0 | C | G | 25.7% | 62.1 / 23.4 | 35 | F207L (TTC→TTG) | bamA‑I | outer membrane protein assembly factor |
| * | NC_002947 | 3,822,630 | 0 | C | G | 25.0% | 79.2 / 29.8 | 44 | F207L (TTC→TTG) | bamA‑II | outer membrane protein assembly factor |
| * | NC_002947 | 196,390 | 0 | T | C | 23.6% | 607.3 / 192.1 | 314 | D632D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 668,074 | 0 | T | G | 23.5% | 599.2 / 42.5 | 287 | intergenic (+35/+117) | yfhM/PP_0571 | lipoprotein/membrane protein |
| * | NC_002947 | 197,590 | 0 | T | C | 23.5% | 799.1 / 250.8 | 423 | D1032D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 2,365,388 | 0 | C | G | 23.2% | 709.6 / 47.8 | 310 | R254P (CGC→CCC) | PP_2075 | membrane protein |
| * | NC_002947 | 1,206,967 | 0 | A | C | 22.8% | 1006.5 / 28.3 | 406 | Q139P (CAG→CCG) | xcpW | type II secretion pathway protein XcpW |
| * | NC_002947 | 5,729,306 | 0 | T | G | 22.7% | 532.1 / 23.5 | 266 | intergenic (‑203/+91) | PP_5024/opgH | amino acid ABC transporter substrate‑binding protein/glucans biosynthesis glucosyltransferase H |
| Marginal new junction evidence (lowest skew 10 of 568 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | 4813168 = | 40 (0.100) | 159 (0.500) | 58/226 | 8.4 | 58.2% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5993940 | 198 (0.620) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 1785057 | 229 (0.550) | 74 (0.190) | 53/282 | 12.6 | 27.0% | intergenic (+25/+81) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase |
| ? | NC_002947 | 1785120 = | 182 (0.460) | intergenic (+88/+18) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase | |||||
| * | ? | NC_002947 | = 652785 | 477 (1.140) | 101 (0.280) | 46/256 | 12.9 | 32.8% | coding (1961/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947 | = 4813153 | 2 (0.010) | intergenic (‑268/‑287) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947 | = 5206564 | 254 (0.610) | 88 (0.220) | 52/290 | 13.3 | 31.7% | intergenic (‑53/‑127) | PP_4582/PP_4583 | membrane protein/putative Peptidase |
| ? | NC_002947 | 5206663 = | 130 (0.320) | intergenic (‑152/‑28) | PP_4582/PP_4583 | membrane protein/putative Peptidase | |||||
| * | ? | NC_002947 | = 4813173 | 24 (0.060) | 161 (0.420) | 48/272 | 13.3 | 52.6% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 5993770 = | 268 (0.700) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 5993776 | 319 (0.760) | 41 (0.100) | 31/280 | 18.6 | 12.6% | intergenic (+65/‑481) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947 | 5993968 = | 270 (0.680) | intergenic (+257/‑289) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 6065449 | 281 (0.670) | 23 (0.060) | 14/268 | 25.3 | 8.1% | intergenic (+80/+101) | PP_5311/PP_5312 | signal transduction protein/hypothetical protein |
| ? | NC_002947 | = 6065508 | 268 (0.710) | intergenic (+139/+42) | PP_5311/PP_5312 | signal transduction protein/hypothetical protein | |||||
| * | ? | NC_002947 | = 2263051 | NA (NA) | 38 (0.100) | 15/280 | 25.4 | 19.0% | intergenic (+114/‑278) | PP_1990/asd | transposase/aspartate‑semialdehyde dehydrogenase |
| ? | NC_002947 | = 2263144 | 171 (0.410) | intergenic (+207/‑185) | PP_1990/asd | transposase/aspartate‑semialdehyde dehydrogenase | |||||
| * | ? | NC_002947 | 2315516 = | 412 (0.990) | 29 (0.070) | 14/276 | 25.7 | 6.7% | coding (275/1311 nt) | PP_2033 | hypothetical protein |
| ? | NC_002947 | 2315573 = | 429 (1.100) | coding (332/1311 nt) | PP_2033 | hypothetical protein | |||||
| * | ? | NC_002947 | 1491962 = | 270 (0.650) | 16 (0.050) | 10/236 | 25.8 | 7.1% | intergenic (+22/+108) | yhdZ/degS | amino acid ABC transporter ATP‑binding protein/serine endoprotease DegS |
| ? | NC_002947 | 1492052 = | 204 (0.610) | intergenic (+112/+18) | yhdZ/degS | amino acid ABC transporter ATP‑binding protein/serine endoprotease DegS | |||||