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 215 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 | . | 56.3% | 218.4 / inf | 744 | coding (1846/26049 nt) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 4,353,698 | 0 | A | G | 51.1% | 200.6 / inf | 816 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 5,227,990 | 0 | A | C | 50.0% | ‑6.5 / 15.6 | 22 | L435R (CTG→CGG) | PP_4603 | transposase |
| * | NC_002947 | 699,725 | 0 | A | G | 48.9% | 131.2 / inf | 543 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 1,332,076 | 0 | C | T | 48.8% | 372.8 / inf | 740 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 5,227,996 | 0 | C | G | 45.8% | ‑6.1 / 10.6 | 24 | R433P (CGG→CCG) | PP_4603 | transposase |
| * | NC_002947 | 5,745,472 | 0 | T | G | 42.6% | 150.5 / inf | 329 | intergenic (+32/+39) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947 | 5,745,476 | 0 | A | T | 42.5% | 138.6 / inf | 318 | intergenic (+36/+35) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947 | 4,345,075 | 0 | C | T | 42.1% | 193.9 / 286.7 | 243 | intergenic (+67/‑264) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 1,549,492 | 0 | G | C | 42.1% | 335.5 / inf | 453 | intergenic (+60/+54) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 4,813,174 | 0 | A | C | 42.1% | 101.1 / 226.9 | 172 | intergenic (‑289/‑266) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 4,345,076 | 0 | A | G | 42.0% | 201.2 / 285.2 | 243 | intergenic (+68/‑263) | 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 | 42.0% | 199.7 / 289.5 | 243 | intergenic (+69/‑262) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 1,549,480 | 0 | C | A | 41.9% | 291.0 / inf | 449 | intergenic (+48/+66) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 4,813,175 | 0 | A | G | 41.5% | 101.2 / 197.2 | 172 | intergenic (‑290/‑265) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 1,549,495 | 0 | T | G | 41.4% | 307.6 / inf | 469 | intergenic (+63/+51) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 195,634 | 0 | C | T | 41.2% | 692.9 / inf | 881 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 4,345,074 | 0 | A | G | 41.0% | 222.4 / 284.8 | 254 | intergenic (+66/‑265) | 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 | 40.1% | 304.2 / inf | 427 | intergenic (‑162/+67) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 3,822,630 | 0 | C | G | 40.0% | 47.1 / 59.8 | 50 | F207L (TTC→TTG) | bamA‑II | outer membrane protein assembly factor |
| Marginal new junction evidence (lowest skew 10 of 1219 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | 4813168 = | 108 (0.220) | 263 (0.700) | 87/214 | 4.4 | 54.7% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5993940 | 354 (0.940) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 652785 | 474 (0.950) | 277 (0.650) | 90/244 | 5.7 | 57.7% | 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 | 101 (0.200) | 274 (0.600) | 96/260 | 5.8 | 50.1% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 5993770 = | 454 (0.990) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 4813173 | 101 (0.200) | 190 (0.440) | 68/244 | 9.3 | 41.4% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5993954 | 452 (1.050) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | 4813168 = | 108 (0.220) | 185 (0.450) | 53/232 | 11.7 | 42.8% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 5993784 = | 406 (1.000) | intergenic (+73/‑473) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 4591049 | 269 (0.540) | 112 (0.310) | 45/208 | 12.1 | 38.8% | intergenic (+139/+78) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947 | = 4591077 | 157 (0.430) | intergenic (+167/+50) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947 | = 6011579 | 271 (0.540) | 104 (0.280) | 37/212 | 14.7 | 35.4% | intergenic (+42/+57) | ydcJ/PP_5261 | metalloprotein/LysR family transcriptional regulator |
| ? | NC_002947 | = 6011591 | 178 (0.480) | intergenic (+54/+45) | ydcJ/PP_5261 | metalloprotein/LysR family transcriptional regulator | |||||
| * | ? | NC_002947 | = 176399 | NA (NA) | 149 (0.310) +CGAAA |
52/274 | 14.7 | 28.4% | intergenic (+43/‑420) | PP_5SA/PP_16SB | 5S ribosomal RNA/16S ribosomal RNA |
| ? | NC_002947 | = 182013 | 390 (0.780) | intergenic (+2/+63) | PP_5SB/PP_0160 | 5S ribosomal RNA/ferrioxamine receptor | |||||
| * | ? | NC_002947 | = 5458135 | 61 (0.120) | 68 (0.210) +48 bp |
31/188 | 14.8 | 33.7% | intergenic (+151/‑204) | lnt/PP_4791 | apolipoprotein N‑acyltransferase/transposase |
| ? | NC_002947 | 5550623 = | 344 (0.690) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||
| * | ? | NC_002947 | 5229497 = | 44 (0.090) | 68 (0.210) +48 bp |
31/188 | 14.8 | 34.7% | intergenic (‑204/+175) | PP_4603/PP_4604 | transposase/DMT superfamily permease |
| ? | NC_002947 | 5550623 = | 344 (0.690) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||