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 178 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 4,348,749 | 0 | A | G | 56.3% | 15.0 / inf | 444 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 1,327,127 | 0 | C | T | 52.3% | 143.4 / inf | 453 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 699,725 | 0 | A | G | 51.1% | ‑4.4 / inf | 370 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 4,808,226 | 0 | A | G | 48.2% | 3.4 / 75.4 | 57 | 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 | 47.4% | 5.1 / 82.5 | 57 | intergenic (‑289/‑266) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 4,340,125 | 0 | A | G | 44.4% | 83.1 / 152.4 | 130 | intergenic (+66/‑265) | 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 | 43.4% | 87.3 / 149.1 | 124 | 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 | 43.1% | 81.6 / 153.4 | 124 | intergenic (+69/‑262) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,340,133 | 0 | G | C | 42.6% | 112.3 / 171.0 | 131 | intergenic (+74/‑257) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,340,134 | 0 | A | T | 42.4% | 106.5 / 153.6 | 129 | intergenic (+75/‑256) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,340,126 | 0 | C | T | 41.6% | 96.7 / 148.1 | 128 | intergenic (+67/‑264) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 195,634 | 0 | C | T | 41.0% | 398.0 / inf | 514 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 4,340,120 | 0 | G | C | 40.3% | 141.0 / 177.3 | 141 | intergenic (+61/‑270) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 2,282,813 | 0 | T | G | 39.9% | 144.1 / 255.2 | 203 | intergenic (‑162/+67) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 4,340,119 | 0 | A | T | 39.9% | 149.4 / 167.3 | 152 | intergenic (+60/‑271) | 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 | 39.1% | 167.1 / 225.0 | 184 | intergenic (‑171/+58) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 3,817,681 | 0 | C | G | 37.8% | 44.0 / 37.4 | 37 | F207L (TTC→TTG) | bamA‑II | outer membrane protein assembly factor |
| * | NC_002947 | 2,282,818 | 0 | G | C | 37.5% | 180.4 / 205.7 | 178 | intergenic (‑167/+62) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 2,282,817 | 0 | G | C | 37.3% | 179.6 / 209.4 | 178 | intergenic (‑166/+63) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 5,740,527 | 0 | A | T | 37.1% | 80.5 / 130.8 | 136 | intergenic (+36/+35) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| Marginal new junction evidence (lowest skew 10 of 467 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | 4808219 = | 42 (0.140) | 133 (0.590) | 55/222 | 5.2 | 58.0% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5988991 | 161 (0.720) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 4808224 | 30 (0.100) | 123 (0.450) | 48/268 | 9.0 | 52.8% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 5988821 = | 192 (0.710) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 4808224 | 30 (0.100) | 129 (0.510) | 28/252 | 13.9 | 53.3% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5989005 | 200 (0.790) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 1970782 | 206 (0.700) | 47 (0.180) | 27/252 | 14.3 | 19.7% | intergenic (+33/‑233) | mtnA/PP_mr25 | methylthioribose‑1‑phosphate isomerase/gyrA regulatory region |
| ? | NC_002947 | = 1970844 | 206 (0.810) | intergenic (+95/‑171) | mtnA/PP_mr25 | methylthioribose‑1‑phosphate isomerase/gyrA regulatory region | |||||
| * | ? | NC_002947 | 4586063 = | 144 (0.490) | 47 (0.220) | 21/216 | 14.4 | 35.3% | intergenic (+102/+115) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947 | 4586167 = | 66 (0.300) | intergenic (+206/+11) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947 | 5743392 = | 216 (0.730) | 53 (0.200) | 28/266 | 14.7 | 21.6% | intergenic (‑169/+78) | fbp/glgP | class 1 fructose‑1,6‑bisphosphatase/glycogen phosphorylase |
| ? | NC_002947 | 5743446 = | 189 (0.700) | intergenic (‑223/+24) | fbp/glgP | class 1 fructose‑1,6‑bisphosphatase/glycogen phosphorylase | |||||
| * | ? | NC_002947 | 1419553 = | 167 (0.570) | 45 (0.200) | 22/228 | 14.7 | 27.7% | intergenic (‑36/+101) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein |
| ? | NC_002947 | 1419647 = | 104 (0.450) | intergenic (‑130/+7) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein | |||||
| * | ? | NC_002947 | 6006595 = | 117 (0.400) | 43 (0.190) | 20/220 | 15.1 | 34.0% | intergenic (+7/+92) | ydcJ/PP_5261 | metalloprotein/LysR family transcriptional regulator |
| ? | NC_002947 | 6006679 = | 79 (0.360) | intergenic (+91/+8) | ydcJ/PP_5261 | metalloprotein/LysR family transcriptional regulator | |||||
| * | ? | NC_002947 | = 4896443 | 155 (0.530) | 48 (0.190) | 23/250 | 15.7 | 25.4% | intergenic (+31/‑177) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein |
| ? | NC_002947 | = 4896490 | 150 (0.590) | intergenic (+78/‑130) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein | |||||
| * | ? | NC_002947 | 5914213 = | 184 (0.620) | 38 (0.160) | 20/236 | 16.1 | 20.9% | intergenic (+49/+104) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase |
| ? | NC_002947 | 5914309 = | 138 (0.580) | intergenic (+145/+8) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase | |||||