mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 43 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 1,499,497 | 1 | . | C | 70.0% | 359.6 / 241.0 | 207 | intergenic (+74/‑90) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| * | NC_002947 | 1,499,498 | 0 | T | G | 69.9% | 229.4 / 213.8 | 207 | intergenic (+75/‑89) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| * | NC_002947 | 4,808,180 | 0 | A | . | 68.0% | ‑3.0 / 54.3 | 32 | intergenic (‑289/‑266) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 4,741,228 | 1 | . | C | 63.9% | 43.8 / 51.4 | 36 | intergenic (+465/+288) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,230 | 0 | A | G | 63.9% | ‑5.8 / 29.2 | 36 | intergenic (+467/+286) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 699,722 | 0 | A | G | 61.1% | 7.3 / 270.9 | 267 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 4,808,179 | 0 | G | . | 56.7% | 25.6 / 68.3 | 31 | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 1,327,121 | 0 | C | T | 48.8% | 157.5 / inf | 292 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 4,348,705 | 0 | A | G | 45.9% | 179.3 / inf | 314 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 195,634 | 0 | C | T | 42.9% | 50.4 / 272.0 | 262 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 4,808,176 | 0 | C | . | 41.7% | 29.2 / 38.0 | 24 | intergenic (‑285/‑270) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 4,808,177 | 0 | G | . | 41.7% | 9.7 / 37.6 | 24 | intergenic (‑286/‑269) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 4,808,178 | 0 | C | . | 41.7% | 33.4 / 38.0 | 24 | intergenic (‑287/‑268) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 4,741,229 | 0 | A | C | 36.1% | 30.4 / 25.3 | 36 | intergenic (+466/+287) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,808,171 | 0 | C | . | 35.7% | 30.4 / 37.1 | 28 | intergenic (‑280/‑275) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 4,808,172 | 0 | C | . | 35.7% | 45.4 / 37.1 | 28 | intergenic (‑281/‑274) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 4,808,173 | 0 | G | . | 35.7% | 10.4 / 36.8 | 28 | intergenic (‑282/‑273) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 4,808,174 | 0 | C | . | 35.7% | 37.4 / 37.1 | 28 | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 4,808,175 | 0 | C | . | 35.7% | 40.1 / 37.1 | 28 | intergenic (‑284/‑271) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 4,808,170 | 0 | G | . | 30.3% | 17.0 / 35.9 | 33 | intergenic (‑279/‑276) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| Marginal new junction evidence (lowest skew 10 of 15 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | = 4808174 | 19 (0.090) | 61 (0.300) | 33/226 | 11.9 | 79.9% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 4808189 = | 13 (0.060) | intergenic (‑298/‑257) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947 | 4808174 = | 38 (0.180) | 35 (0.230) | 19/172 | 13.3 | 35.5% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5988935 | 100 (0.660) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | 1070247 = | 205 (0.960) | 52 (0.270) | 24/216 | 14.3 | 32.8% | intergenic (+47/+95) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| ? | NC_002947 | = 4808161 | 30 (0.160) | intergenic (‑270/‑285) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947 | = 4808179 | 11 (0.050) | 66 (0.310) | 23/240 | 16.0 | 79.6% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 4808194 = | 23 (0.110) | intergenic (‑303/‑252) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947 | = 652783 | 220 (1.030) | 23 (0.150) | 13/172 | 16.1 | 21.0% | coding (1960/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947 | 4808209 = | 17 (0.110) | intergenic (‑318/‑237) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947 | 4808174 = | 38 (0.180) | 24 (0.140) | 13/190 | 17.4 | 29.8% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 5988779 = | 83 (0.490) | intergenic (+73/‑473) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 4808179 | 17 (0.080) | 31 (0.220) +43 bp |
6/156 | 19.3 | 49.5% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 4808259 = | 81 (0.380) | intergenic (‑368/‑187) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947 | = 4808174 | 35 (0.160) | 23 (0.110) | 9/228 | 22.0 | 20.6% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 4945201 | 144 (0.710) | intergenic (+561/+237) | PP_5673/flhB | D‑alanine‑‑D‑alanine ligase/flagellin export apparatus substrate specificity protein | |||||
| * | ? | NC_002947 | 1683236 = | 210 (0.980) | 31 (0.170) | 7/208 | 22.2 | 24.1% | intergenic (+45/‑186) | recJ/PP_1478 | ssDNA‑specific exonuclease RecJ/xenobiotic reductase |
| ? | NC_002947 | = 4808162 | 15 (0.080) | intergenic (‑271/‑284) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947 | = 4808174 | 36 (0.170) | 22 (0.120) | 6/214 | 23.3 | 15.0% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 5737599 = | 217 (1.140) | intergenic (‑154/+48) | hutU/PP_5034 | urocanate hydratase/hypothetical protein | |||||