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 183 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 | 54.1% | 81.9 / inf | 369 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 699,725 | 0 | A | G | 53.5% | 12.3 / inf | 289 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 4,348,749 | 0 | A | G | 52.8% | 80.7 / inf | 426 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 4,808,225 | 0 | A | C | 45.6% | 10.4 / 80.9 | 57 | intergenic (‑289/‑266) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 4,808,226 | 0 | A | G | 45.6% | 16.1 / 71.5 | 57 | intergenic (‑290/‑265) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 1,544,543 | 0 | G | C | 44.6% | 94.9 / 259.7 | 193 | intergenic (+60/+54) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,544,531 | 0 | C | A | 43.5% | 105.8 / 256.0 | 201 | intergenic (+48/+66) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,544,546 | 0 | T | G | 42.4% | 97.6 / 255.3 | 205 | intergenic (+63/+51) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 5,740,527 | 0 | A | T | 39.8% | 66.2 / 116.0 | 124 | intergenic (+36/+35) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947 | 195,634 | 0 | C | T | 39.4% | 316.4 / inf | 383 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 1,544,534 | 0 | G | C | 39.1% | 166.8 / 254.1 | 202 | intergenic (+51/+63) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,544,536 | 0 | C | G | 38.9% | 172.2 / 242.8 | 193 | intergenic (+53/+61) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,544,541 | 0 | C | G | 38.9% | 170.7 / 241.1 | 193 | intergenic (+58/+56) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,013,251 | 0 | A | T | 37.6% | 184.9 / 193.2 | 189 | intergenic (+76/+55) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947 | 1,013,252 | 0 | T | G | 37.2% | 198.3 / 205.8 | 186 | intergenic (+77/+54) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947 | 358,099 | 0 | C | T | 36.4% | 112.5 / 120.3 | 132 | intergenic (+64/‑66) | tdcG‑I/PP_5441 | L‑serine dehydratase/hypothetical protein |
| * | NC_002947 | 358,094 | 0 | G | A | 35.8% | 103.8 / 120.5 | 127 | intergenic (+59/‑71) | tdcG‑I/PP_5441 | L‑serine dehydratase/hypothetical protein |
| * | NC_002947 | 1,013,245 | 0 | G | C | 35.8% | 240.1 / 214.1 | 195 | intergenic (+70/+61) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947 | 1,013,238 | 0 | A | T | 35.6% | 217.8 / 192.0 | 191 | intergenic (+63/+68) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947 | 2,282,813 | 0 | T | G | 35.6% | 144.2 / 182.0 | 163 | intergenic (‑162/+67) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| Marginal new junction evidence (lowest skew 10 of 676 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | = 4808224 | 31 (0.130) | 139 (0.620) | 54/270 | 6.0 | 59.6% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 5988821 = | 160 (0.710) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | 4808219 = | 45 (0.180) | 111 (0.600) | 43/224 | 6.1 | 56.8% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5988991 | 135 (0.730) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 652785 | 232 (0.950) | 95 (0.450) | 49/254 | 6.3 | 48.7% | 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 | 31 (0.130) | 123 (0.580) | 35/254 | 9.6 | 56.7% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5989005 | 161 (0.760) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | 4647603 = | 104 (0.420) | 45 (0.250) | 17/216 | 14.0 | 34.1% | intergenic (+10/+121) | fusB/PP_4112 | elongation factor G 2/sulfate transporter |
| ? | NC_002947 | 4647711 = | 98 (0.550) | intergenic (+118/+13) | fusB/PP_4112 | elongation factor G 2/sulfate transporter | |||||
| * | ? | NC_002947 | = 1970782 | 206 (0.840) | 32 (0.150) | 22/254 | 14.1 | 15.1% | intergenic (+33/‑233) | mtnA/PP_mr25 | methylthioribose‑1‑phosphate isomerase/gyrA regulatory region |
| ? | NC_002947 | = 1970844 | 183 (0.870) | intergenic (+95/‑171) | mtnA/PP_mr25 | methylthioribose‑1‑phosphate isomerase/gyrA regulatory region | |||||
| * | ? | NC_002947 | 1967188 = | 129 (0.530) | 33 (0.170) | 16/228 | 15.2 | 24.3% | intergenic (+15/+104) | PP_1762/yciK | hypothetical protein/putative oxidoreductase |
| ? | NC_002947 | 1967284 = | 106 (0.560) | intergenic (+111/+8) | PP_1762/yciK | hypothetical protein/putative oxidoreductase | |||||
| * | ? | NC_002947 | 5201627 = | 89 (0.360) | 37 (0.200) | 14/220 | 15.7 | 38.1% | intergenic (‑65/‑115) | PP_4582/PP_4583 | membrane protein/putative Peptidase |
| ? | NC_002947 | 5201722 = | 54 (0.300) | intergenic (‑160/‑20) | PP_4582/PP_4583 | membrane protein/putative Peptidase | |||||
| * | ? | NC_002947 | = 2050638 | 151 (0.620) | 31 (0.170) | 14/220 | 15.7 | 25.5% | intergenic (‑88/+87) | PP_1824/PP_1825 | Smr domain‑containing protein/hypothetical protein |
| ? | NC_002947 | = 2050674 | 68 (0.370) | intergenic (‑124/+51) | PP_1824/PP_1825 | Smr domain‑containing protein/hypothetical protein | |||||
| * | ? | NC_002947 | 4896423 = | 161 (0.660) | 37 (0.180) | 17/252 | 16.2 | 20.5% | intergenic (+11/‑197) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein |
| ? | NC_002947 | 4896512 = | 149 (0.710) | intergenic (+100/‑108) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein | |||||