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 163 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 | 52.6% | 143.6 / inf | 467 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 699,725 | 0 | A | G | 51.5% | 21.4 / inf | 404 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 4,348,749 | 0 | A | G | 48.9% | 198.0 / inf | 485 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 4,808,226 | 0 | A | G | 43.5% | 16.7 / 54.0 | 47 | 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 | 42.5% | 26.9 / 60.0 | 47 | intergenic (‑289/‑266) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 2,282,813 | 0 | T | G | 41.4% | 140.0 / 312.5 | 241 | intergenic (‑162/+67) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 195,634 | 0 | C | T | 39.5% | 431.5 / inf | 486 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 4,340,125 | 0 | A | G | 38.3% | 107.9 / 113.1 | 109 | intergenic (+66/‑265) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 2,282,822 | 0 | C | A | 37.9% | 212.1 / 288.2 | 235 | intergenic (‑171/+58) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 2,282,818 | 0 | G | C | 37.4% | 217.5 / 270.2 | 222 | intergenic (‑167/+62) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 4,340,126 | 0 | C | T | 37.4% | 112.9 / 111.7 | 107 | intergenic (+67/‑264) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,340,127 | 0 | A | G | 37.4% | 113.9 / 110.8 | 107 | intergenic (+68/‑263) | 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% | 113.3 / 112.6 | 107 | intergenic (+69/‑262) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 2,282,817 | 0 | G | C | 37.3% | 223.1 / 269.3 | 222 | intergenic (‑166/+63) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 1,544,543 | 0 | G | C | 36.4% | 243.1 / 231.7 | 209 | intergenic (+60/+54) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 4,340,120 | 0 | G | C | 35.7% | 158.2 / 127.8 | 112 | intergenic (+61/‑270) | 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 | 35.4% | 140.4 / 121.0 | 117 | intergenic (+60/‑271) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,852,505 | 0 | A | C | 35.2% | 68.7 / 22.8 | 54 | intergenic (‑131/+166) | recR/ybaB | recombination protein RecR/nucleoid‑associated broad specificity regulator |
| * | NC_002947 | 1,013,252 | 0 | T | G | 35.0% | 205.8 / 182.9 | 179 | intergenic (+77/+54) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947 | 1,013,251 | 0 | A | T | 34.6% | 226.3 / 176.0 | 185 | intergenic (+76/+55) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| Marginal new junction evidence (lowest skew 10 of 522 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | 4808219 = | 32 (0.100) | 111 (0.460) | 46/228 | 7.9 | 55.3% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5988991 | 155 (0.640) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 4808224 | 27 (0.080) | 131 (0.450) | 49/274 | 10.0 | 51.3% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 5988821 = | 224 (0.760) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 652785 | 321 (1.010) | 80 (0.290) | 42/258 | 10.9 | 36.6% | 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 | 27 (0.080) | 111 (0.400) | 30/258 | 14.8 | 48.9% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5989005 | 209 (0.760) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | 4647603 = | 117 (0.370) | 54 (0.230) | 20/220 | 16.4 | 35.0% | intergenic (+10/+121) | fusB/PP_4112 | elongation factor G 2/sulfate transporter |
| ? | NC_002947 | 4647711 = | 114 (0.480) | intergenic (+118/+13) | fusB/PP_4112 | elongation factor G 2/sulfate transporter | |||||
| * | ? | NC_002947 | 4586063 = | 146 (0.460) | 30 (0.130) | 17/222 | 18.1 | 24.5% | intergenic (+102/+115) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947 | 4586167 = | 76 (0.320) | intergenic (+206/+11) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947 | 5162618 = | 133 (0.420) | 36 (0.140) | 17/246 | 19.8 | 22.5% | intergenic (+93/+108) | PP_4544/PP_4545 | hypothetical protein/beta‑ketodecanoyl‑ACP synthase |
| ? | NC_002947 | 5162702 = | 139 (0.530) | intergenic (+177/+24) | PP_4544/PP_4545 | hypothetical protein/beta‑ketodecanoyl‑ACP synthase | |||||
| * | ? | NC_002947 | = 511921 | 214 (0.670) | 32 (0.110) | 20/268 | 19.8 | 14.4% | intergenic (+58/‑90) | trpC/PP_0423 | indole‑3‑glycerol phosphate synthase/hypothetical protein |
| ? | NC_002947 | = 511969 | 188 (0.660) | intergenic (+106/‑42) | trpC/PP_0423 | indole‑3‑glycerol phosphate synthase/hypothetical protein | |||||
| * | ? | NC_002947 | 4896423 = | 189 (0.590) | 38 (0.140) | 18/256 | 20.0 | 19.0% | intergenic (+11/‑197) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein |
| ? | NC_002947 | 4896512 = | 161 (0.590) | intergenic (+100/‑108) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein | |||||
| * | ? | NC_002947 | 1114875 = | 176 (0.550) | 32 (0.120) | 17/248 | 20.0 | 17.2% | intergenic (‑64/+115) | rlmF/valS | ribosomal RNA large subunit methyltransferase F/valine‑‑tRNA ligase |
| ? | NC_002947 | 1114951 = | 163 (0.610) | intergenic (‑140/+39) | rlmF/valS | ribosomal RNA large subunit methyltransferase F/valine‑‑tRNA ligase | |||||