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 | 1,327,127 | 0 | C | T | 53.8% | 127.1 / inf | 624 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 4,810,148 | 0 | A | G | 53.0% | 9.1 / 112.1 | 84 | intergenic (‑290/‑265) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 4,810,147 | 0 | A | C | 52.4% | 15.0 / 121.0 | 84 | intergenic (‑289/‑266) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 5,224,969 | 0 | C | G | 52.2% | ‑5.6 / 25.4 | 23 | R433P (CGG→CCG) | PP_4603 | transposase |
| * | NC_002947 | 4,350,671 | 0 | A | G | 51.8% | 155.7 / inf | 668 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 699,725 | 0 | A | G | 43.5% | 286.2 / inf | 489 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 195,634 | 0 | C | T | 41.6% | 487.4 / inf | 665 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 1,544,531 | 0 | C | A | 40.0% | 248.7 / inf | 277 | intergenic (+48/+66) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,544,543 | 0 | G | C | 39.1% | 265.4 / inf | 274 | intergenic (+60/+54) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,544,546 | 0 | T | G | 38.8% | 244.7 / inf | 276 | intergenic (+63/+51) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 4,342,047 | 0 | A | G | 37.5% | 123.6 / 115.5 | 112 | intergenic (+66/‑265) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 1,544,536 | 0 | C | G | 37.4% | 322.8 / inf | 274 | intergenic (+53/+61) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 4,342,048 | 0 | C | T | 36.9% | 124.2 / 113.8 | 111 | intergenic (+67/‑264) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,342,049 | 0 | A | G | 36.9% | 127.3 / 112.3 | 111 | intergenic (+68/‑263) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,342,050 | 0 | C | T | 36.9% | 124.2 / 115.2 | 111 | intergenic (+69/‑262) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 1,544,541 | 0 | C | G | 36.9% | 331.4 / inf | 274 | intergenic (+58/+56) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,544,534 | 0 | G | C | 36.7% | 352.1 / inf | 290 | intergenic (+51/+63) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 4,342,055 | 0 | G | C | 35.0% | 174.1 / 130.2 | 117 | intergenic (+74/‑257) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,342,042 | 0 | G | C | 34.4% | 193.5 / 131.1 | 122 | intergenic (+61/‑270) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 1,013,252 | 0 | T | G | 34.4% | 295.5 / 235.5 | 234 | intergenic (+77/+54) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| Marginal new junction evidence (lowest skew 10 of 379 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | 4810141 = | 71 (0.180) | 178 (0.600) | 66/224 | 6.1 | 58.5% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5990913 | 199 (0.680) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 4810146 | 41 (0.110) | 204 (0.570) | 64/270 | 9.5 | 59.0% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 5990743 = | 246 (0.690) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 652785 | 356 (0.920) | 144 (0.430) | 59/254 | 9.5 | 48.3% | coding (1961/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947 | = 4810126 | 1 (0.000) | intergenic (‑268/‑287) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947 | = 2052560 | 221 (0.570) | 47 (0.160) | 21/220 | 19.9 | 24.1% | intergenic (‑88/+87) | PP_1824/PP_1825 | Smr domain‑containing protein/hypothetical protein |
| ? | NC_002947 | = 2052596 | 131 (0.450) | intergenic (‑124/+51) | PP_1824/PP_1825 | Smr domain‑containing protein/hypothetical protein | |||||
| * | ? | NC_002947 | 4587985 = | 150 (0.390) | 48 (0.170) | 20/218 | 20.2 | 34.1% | intergenic (+102/+115) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947 | 4588089 = | 74 (0.260) | intergenic (+206/+11) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947 | 4649525 = | 149 (0.390) | 52 (0.180) | 19/216 | 20.6 | 28.5% | intergenic (+10/+121) | fusB/PP_4112 | elongation factor G 2/sulfate transporter |
| ? | NC_002947 | 4649633 = | 152 (0.540) | intergenic (+118/+13) | fusB/PP_4112 | elongation factor G 2/sulfate transporter | |||||
| * | ? | NC_002947 | = 4898365 | 191 (0.490) | 65 (0.200) | 23/252 | 21.5 | 26.3% | intergenic (+31/‑177) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein |
| ? | NC_002947 | = 4898412 | 200 (0.600) | intergenic (+78/‑130) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein | |||||
| * | ? | NC_002947 | = 1970782 | 275 (0.710) | 52 (0.160) | 23/254 | 21.6 | 16.9% | intergenic (+33/‑233) | mtnA/PP_mr25 | methylthioribose‑1‑phosphate isomerase/gyrA regulatory region |
| ? | NC_002947 | = 1970844 | 275 (0.820) | intergenic (+95/‑171) | mtnA/PP_mr25 | methylthioribose‑1‑phosphate isomerase/gyrA regulatory region | |||||
| * | ? | NC_002947 | 1970763 = | 288 (0.750) | 49 (0.150) | 23/254 | 21.6 | 16.0% | intergenic (+14/‑252) | mtnA/PP_mr25 | methylthioribose‑1‑phosphate isomerase/gyrA regulatory region |
| ? | NC_002947 | 1970865 = | 264 (0.790) | intergenic (+116/‑150) | mtnA/PP_mr25 | methylthioribose‑1‑phosphate isomerase/gyrA regulatory region | |||||
| * | ? | NC_002947 | 1899249 = | 314 (0.810) | 53 (0.150) | 26/274 | 21.7 | 15.2% | intergenic (+277/‑243) | PP_t18/PP_1703 | tRNA‑Asp/assimilatory nitrate reductase/sulfite reductase |
| ? | NC_002947 | 1899331 = | 298 (0.830) | intergenic (+359/‑161) | PP_t18/PP_1703 | tRNA‑Asp/assimilatory nitrate reductase/sulfite reductase | |||||