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 149 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 699,725 | 0 | A | G | 49.9% | 81.1 / inf | 565 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 4,348,749 | 0 | A | G | 49.6% | 286.9 / inf | 749 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 1,327,127 | 0 | C | T | 49.0% | 314.8 / inf | 627 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 5,223,003 | 0 | G | T | 47.6% | ‑5.7 / 11.0 | 21 | intergenic (‑366/+13) | PP_4602/PP_4603 | AraC family transcriptional regulator/transposase |
| * | NC_002947 | 4,808,226 | 0 | A | G | 40.9% | 64.8 / 119.8 | 106 | intergenic (‑290/‑265) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 4,808,225 | 0 | A | C | 40.6% | 72.7 / 137.1 | 106 | intergenic (‑289/‑266) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 5,223,012 | 0 | G | C | 40.0% | ‑5.1 / 10.1 | 30 | intergenic (‑375/+4) | PP_4602/PP_4603 | AraC family transcriptional regulator/transposase |
| * | NC_002947 | 4,340,125 | 0 | A | G | 38.1% | 166.4 / 163.0 | 156 | intergenic (+66/‑265) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 5,223,064 | 0 | A | C | 37.8% | ‑4.1 / 10.2 | 45 | A427A (GCT→GCG) | PP_4603 | transposase |
| * | NC_002947 | 195,634 | 0 | C | T | 37.8% | 721.9 / inf | 755 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 4,340,127 | 0 | A | G | 37.7% | 167.3 / 160.9 | 155 | intergenic (+68/‑263) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 1,544,543 | 0 | G | C | 37.6% | 374.7 / inf | 343 | intergenic (+60/+54) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,544,531 | 0 | C | A | 37.5% | 360.4 / inf | 341 | intergenic (+48/+66) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 4,340,126 | 0 | C | T | 37.4% | 166.5 / 163.5 | 155 | intergenic (+67/‑264) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,340,128 | 0 | C | T | 37.4% | 168.7 / 160.6 | 155 | intergenic (+69/‑262) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 1,544,546 | 0 | T | G | 35.9% | 373.2 / inf | 370 | intergenic (+63/+51) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 2,282,813 | 0 | T | G | 35.6% | 285.1 / 287.0 | 266 | intergenic (‑162/+67) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 1,544,534 | 0 | G | C | 34.9% | 446.8 / inf | 344 | intergenic (+51/+63) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 4,340,133 | 0 | G | C | 34.7% | 260.6 / 188.2 | 173 | intergenic (+74/‑257) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,340,119 | 0 | A | T | 34.4% | 263.3 / 177.3 | 187 | intergenic (+60/‑271) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| Marginal new junction evidence (lowest skew 10 of 267 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | 4808219 = | 62 (0.130) | 207 (0.590) | 75/226 | 5.2 | 59.0% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5988991 | 241 (0.680) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 652785 | 412 (0.890) | 154 (0.390) | 60/256 | 10.1 | 46.2% | coding (1961/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947 | = 4808204 | 2 (0.010) | intergenic (‑268/‑287) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947 | = 4808224 | 65 (0.140) | 230 (0.540) | 62/272 | 10.7 | 59.2% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 5988821 = | 258 (0.610) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | 4647603 = | 170 (0.370) | 74 (0.220) | 26/218 | 17.9 | 33.1% | intergenic (+10/+121) | fusB/PP_4112 | elongation factor G 2/sulfate transporter |
| ? | NC_002947 | 4647711 = | 174 (0.510) | intergenic (+118/+13) | fusB/PP_4112 | elongation factor G 2/sulfate transporter | |||||
| * | ? | NC_002947 | = 5513315 | 483 (1.040) | 56 (0.150) | 28/244 | 19.1 | 12.8% | intergenic (+45/‑109) | urtD/urtE | ABC transporter ATP‑binding protein/ABC transporter ATP‑binding protein |
| ? | NC_002947 | = 5513371 | 368 (0.970) | intergenic (+101/‑53) | urtD/urtE | ABC transporter ATP‑binding protein/ABC transporter ATP‑binding protein | |||||
| * | ? | NC_002947 | 4896423 = | 276 (0.600) | 63 (0.160) | 28/254 | 19.9 | 22.3% | intergenic (+11/‑197) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein |
| ? | NC_002947 | 4896512 = | 202 (0.510) | intergenic (+100/‑108) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein | |||||
| * | ? | NC_002947 | = 5333257 | 621 (1.340) | 61 (0.150) | 28/266 | 20.7 | 10.3% | intergenic (+41/‑202) | gluQ/PP_5704 | glutamyl‑Q tRNA(Asp) synthetase/hypothetical protein |
| ? | NC_002947 | = 5333287 | 504 (1.210) | intergenic (+71/‑172) | gluQ/PP_5704 | glutamyl‑Q tRNA(Asp) synthetase/hypothetical protein | |||||
| * | ? | NC_002947 | 1487013 = | 241 (0.520) | 72 (0.200) | 23/236 | 20.7 | 28.2% | intergenic (+22/+108) | yhdZ/degS | amino acid ABC transporter ATP‑binding protein/serine endoprotease DegS |
| ? | NC_002947 | 1487103 = | 174 (0.470) | intergenic (+112/+18) | yhdZ/degS | amino acid ABC transporter ATP‑binding protein/serine endoprotease DegS | |||||
| * | ? | NC_002947 | = 5594170 | 374 (0.810) | 73 (0.190) | 22/240 | 21.5 | 19.3% | intergenic (‑66/+79) | PP_4921/thiC | NCS1 family transporter/phosphomethylpyrimidine synthase |
| ? | NC_002947 | = 5594207 | 309 (0.820) | intergenic (‑103/+42) | PP_4921/thiC | NCS1 family transporter/phosphomethylpyrimidine synthase | |||||
| * | ? | NC_002947 | = 5692618 | 705 (1.520) | 76 (0.180) | 27/274 | 21.7 | 10.5% | intergenic (+31/‑139) | PP_4994/PP_4995 | hypothetical protein/exopolysaccharide biosynthesis protein |
| ? | NC_002947 | = 5692680 | 647 (1.510) | intergenic (+93/‑77) | PP_4994/PP_4995 | hypothetical protein/exopolysaccharide biosynthesis protein | |||||