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 176 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 | 51.2% | 53.5 / inf | 455 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 1,327,127 | 0 | C | T | 49.6% | 236.3 / inf | 562 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 4,348,749 | 0 | A | G | 48.4% | 223.0 / inf | 521 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 195,634 | 0 | C | T | 42.1% | 333.5 / inf | 540 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 1,544,531 | 0 | C | A | 38.6% | 221.3 / 285.7 | 254 | intergenic (+48/+66) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 358,094 | 0 | G | A | 37.0% | 113.1 / 134.2 | 136 | intergenic (+59/‑71) | tdcG‑I/PP_5441 | L‑serine dehydratase/hypothetical protein |
| * | NC_002947 | 358,093 | 0 | T | C | 36.8% | 126.9 / 129.3 | 136 | intergenic (+58/‑72) | tdcG‑I/PP_5441 | L‑serine dehydratase/hypothetical protein |
| * | NC_002947 | 2,282,813 | 0 | T | G | 36.6% | 178.7 / 196.2 | 194 | intergenic (‑162/+67) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 1,544,546 | 0 | T | G | 36.3% | 278.9 / 264.4 | 260 | intergenic (+63/+51) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,544,534 | 0 | G | C | 36.0% | 321.5 / 270.2 | 262 | intergenic (+51/+63) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,013,252 | 0 | T | G | 35.8% | 227.7 / 219.9 | 207 | intergenic (+77/+54) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947 | 358,088 | 0 | A | G | 34.7% | 157.3 / 129.1 | 147 | intergenic (+53/‑77) | tdcG‑I/PP_5441 | L‑serine dehydratase/hypothetical protein |
| * | NC_002947 | 1,544,543 | 0 | G | C | 34.6% | 299.9 / 262.4 | 254 | intergenic (+60/+54) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,013,251 | 0 | A | T | 34.6% | 249.3 / 209.7 | 218 | intergenic (+76/+55) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947 | 1,544,536 | 0 | C | G | 34.2% | 332.3 / 255.3 | 254 | intergenic (+53/+61) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,544,541 | 0 | C | G | 34.2% | 334.0 / 260.3 | 254 | intergenic (+58/+56) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 358,090 | 0 | C | T | 34.0% | 151.2 / 131.9 | 147 | intergenic (+55/‑75) | tdcG‑I/PP_5441 | L‑serine dehydratase/hypothetical protein |
| * | NC_002947 | 358,097 | 0 | A | G | 33.8% | 171.1 / 126.8 | 149 | intergenic (+62/‑68) | tdcG‑I/PP_5441 | L‑serine dehydratase/hypothetical protein |
| * | NC_002947 | 1,013,245 | 0 | G | C | 33.8% | 305.5 / 226.7 | 226 | intergenic (+70/+61) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947 | 337,839 | 0 | C | T | 33.7% | 241.1 / 176.7 | 203 | intergenic (‑86/+43) | PP_0279/PP_0280 | hypothetical protein/amino acid ABC transporter permease |
| Marginal new junction evidence (lowest skew 10 of 521 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | 4808219 = | 40 (0.120) | 153 (0.600) | 63/226 | 4.5 | 59.5% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5988991 | 178 (0.700) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 4808224 | 45 (0.140) | 163 (0.530) | 57/272 | 7.8 | 51.7% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 5988821 = | 263 (0.860) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 652785 | 336 (1.010) | 102 (0.360) | 47/256 | 9.2 | 41.3% | coding (1961/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947 | = 4808204 | 0 (0.000) | intergenic (‑268/‑287) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947 | = 4808224 | 45 (0.140) | 146 (0.510) | 37/256 | 11.8 | 51.9% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5989005 | 232 (0.810) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | 4896423 = | 162 (0.490) | 49 (0.170) | 26/254 | 15.4 | 24.0% | intergenic (+11/‑197) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein |
| ? | NC_002947 | 4896512 = | 171 (0.600) | intergenic (+100/‑108) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein | |||||
| * | ? | NC_002947 | = 1967220 | 124 (0.370) | 49 (0.190) | 22/230 | 15.5 | 31.2% | intergenic (+47/+72) | PP_1762/yciK | hypothetical protein/putative oxidoreductase |
| ? | NC_002947 | = 1967250 | 120 (0.470) | intergenic (+77/+42) | PP_1762/yciK | hypothetical protein/putative oxidoreductase | |||||
| * | ? | NC_002947 | 4586063 = | 172 (0.520) | 52 (0.210) | 20/220 | 15.7 | 33.6% | intergenic (+102/+115) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947 | 4586167 = | 78 (0.320) | intergenic (+206/+11) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947 | = 1487042 | 192 (0.580) | 46 (0.170) | 22/236 | 15.9 | 23.4% | intergenic (+51/+79) | yhdZ/degS | amino acid ABC transporter ATP‑binding protein/serine endoprotease DegS |
| ? | NC_002947 | = 1487072 | 149 (0.560) | intergenic (+81/+49) | yhdZ/degS | amino acid ABC transporter ATP‑binding protein/serine endoprotease DegS | |||||
| * | ? | NC_002947 | 5903827 = | 234 (0.700) | 55 (0.190) | 25/264 | 16.4 | 20.8% | intergenic (+27/+80) | PP_5176/spuH | hypothetical protein/spermidine/putrescine ABC transporter permease |
| ? | NC_002947 | 5903887 = | 210 (0.710) | intergenic (+87/+20) | PP_5176/spuH | hypothetical protein/spermidine/putrescine ABC transporter permease | |||||
| * | ? | NC_002947 | = 2050638 | 163 (0.490) | 49 (0.200) | 18/222 | 16.8 | 29.0% | intergenic (‑88/+87) | PP_1824/PP_1825 | Smr domain‑containing protein/hypothetical protein |
| ? | NC_002947 | = 2050674 | 118 (0.470) | intergenic (‑124/+51) | PP_1824/PP_1825 | Smr domain‑containing protein/hypothetical protein | |||||