mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 66 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 4,810,147 | 0 | A | C | 62.3% | 36.9 / 60.5 | 53 | intergenic (‑289/‑266) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 4,810,148 | 0 | A | G | 62.3% | 37.7 / 56.0 | 53 | intergenic (‑290/‑265) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 4,350,671 | 0 | A | G | 51.6% | 163.7 / inf | 618 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 699,725 | 0 | A | G | 51.4% | 31.2 / inf | 323 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 1,327,127 | 0 | C | T | 51.2% | 177.4 / inf | 448 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 5,224,969 | 0 | C | G | 50.0% | ‑6.7 / 11.2 | 24 | R433P (CGG→CCG) | PP_4603 | transposase |
| * | NC_002947 | 1,793,445 | 0 | C | G | 48.0% | 23.5 / 75.6 | 50 | F207L (TTC→TTG) | bamA‑I | outer membrane protein assembly factor |
| * | NC_002947 | 4,810,153 | 0 | C | T | 38.6% | 30.8 / 46.4 | 44 | intergenic (‑295/‑260) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 4,810,154 | 0 | G | T | 38.6% | 29.0 / 52.7 | 44 | intergenic (‑296/‑259) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 195,634 | 0 | C | T | 35.9% | 543.5 / inf | 507 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 196,351 | 0 | C | G | 30.7% | 521.6 / inf | 349 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 196,390 | 0 | T | C | 30.4% | 417.5 / 233.1 | 287 | D632D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 5,742,445 | 0 | T | G | 30.0% | 231.4 / 99.7 | 150 | intergenic (+32/+39) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947 | 4,879,291 | 0 | G | C | 29.4% | 454.9 / 84.6 | 228 | intergenic (‑372/‑28) | pucM/puuE | 5‑hydroxyisourate hydrolase/allantoinase |
| * | NC_002947 | 3,445,494 | 0 | T | G | 26.9% | 236.7 / 23.7 | 165 | F763C (TTT→TGT) | PP_3062 | tail length determination protein |
| * | NC_002947 | 196,327 | 0 | A | C | 26.3% | 720.8 / 286.3 | 394 | T611T (ACA→ACC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 3,874,778 | 0 | T | G | 25.7% | 500.3 / 20.2 | 229 | Q443P (CAG→CCG) | PP_3421 | sensor histidine kinase |
| * | NC_002947 | 1,544,401 | 0 | C | G | 25.6% | 575.5 / 84.3 | 274 | A388G (GCG→GGG) | mdfA | multidrug MFS transporter |
| * | NC_002947 | 1,103,902 | 0 | A | T | 25.3% | 547.8 / 45.7 | 264 | D219V (GAT→GTT) | murA | UDP‑N‑acetylglucosamine 1‑carboxyvinyltransferase |
| * | NC_002947 | 5,528,513 | 0 | T | A | 25.2% | 622.2 / 59.9 | 321 | L19Q (CTG→CAG) | PP_4860 | mannose‑6‑phosphate isomerase |
| Marginal new junction evidence (lowest skew 10 of 508 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | 4810141 = | 52 (0.150) | 105 (0.390) | 49/226 | 8.5 | 54.2% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5990913 | 138 (0.520) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 652785 | 370 (1.060) | 98 (0.320) | 50/256 | 10.0 | 37.9% | 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 | = 4810146 | 20 (0.060) | 76 (0.250) | 37/256 | 13.3 | 42.5% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5990927 | 188 (0.620) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 5203537 | 201 (0.580) | 48 (0.140) | 37/290 | 15.1 | 23.1% | intergenic (‑53/‑127) | PP_4582/PP_4583 | membrane protein/putative Peptidase |
| ? | NC_002947 | 5203636 = | 122 (0.360) | intergenic (‑152/‑28) | PP_4582/PP_4583 | membrane protein/putative Peptidase | |||||
| * | ? | NC_002947 | = 1780108 | 136 (0.390) | 41 (0.120) | 33/282 | 16.0 | 23.5% | intergenic (+25/+81) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase |
| ? | NC_002947 | 1780171 = | 137 (0.410) | intergenic (+88/+18) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase | |||||
| * | ? | NC_002947 | = 5990749 | 260 (0.740) | 22 (0.070) | 17/280 | 22.2 | 9.1% | intergenic (+65/‑481) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947 | 5990941 = | 195 (0.590) | intergenic (+257/‑289) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 1025296 | 314 (0.900) | 22 (0.080) | 11/242 | 23.3 | 8.4% | intergenic (‑147/+82) | opdP/dppA‑II | glycine‑glutamate dipeptide porin/dipeptide ABC transporter substrate‑binding protein |
| ? | NC_002947 | = 1025335 | 221 (0.770) | intergenic (‑186/+43) | opdP/dppA‑II | glycine‑glutamate dipeptide porin/dipeptide ABC transporter substrate‑binding protein | |||||
| * | ? | NC_002947 | = 4075881 | NA (NA) | 43 (0.130) | 15/288 | 23.6 | 15.7% | intergenic (‑453/+171) | mdtA/PP_3586 | multidrug transporter membrane fusion protein/transposase |
| ? | NC_002947 | = 4304551 | 238 (0.680) | intergenic (+1075/‑225) | PP_3774/PP_5627 | hypothetical protein/hypothetical protein | |||||
| * | ? | NC_002947 | 1847001 = | 307 (0.880) | 15 (0.060) +40 bp |
8/216 | 23.6 | 6.3% | coding (1250/1377 nt) | pfeS‑II | histidine kinase |
| ? | NC_002947 | 2437200 = | NA (NA) | intergenic (+82/‑222) | PP_2133/PP_2134 | hypothetical protein/transposase | |||||
| * | ? | NC_002947 | 1298272 = | NA (NA) | 43 (0.130) | 15/288 | 23.6 | NA | intergenic (+125/+304) | PP_1133/PP_1134 | transposase/hypothetical protein |
| ? | NC_002947 | 1298318 = | NA (NA) | intergenic (+171/+258) | PP_1133/PP_1134 | transposase/hypothetical protein | |||||