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 64 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 5,224,986 | 0 | A | C | 55.6% | ‑5.3 / 20.5 | 37 | A427A (GCT→GCG) | PP_4603 | transposase |
| * | NC_002947 | 1,327,127 | 0 | C | T | 50.5% | 306.1 / inf | 684 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 5,224,963 | 0 | A | T | 50.0% | ‑6.6 / 19.0 | 30 | L435Q (CTG→CAG) | PP_4603 | transposase |
| * | NC_002947 | 4,350,671 | 0 | A | G | 49.6% | 334.9 / inf | 768 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 5,224,969 | 0 | C | G | 48.5% | ‑6.0 / 12.4 | 34 | R433P (CGG→CCG) | PP_4603 | transposase |
| * | NC_002947 | 699,725 | 0 | A | G | 46.0% | 199.0 / inf | 478 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 4,810,147 | 0 | A | C | 45.6% | 24.5 / 76.8 | 57 | 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 | 45.6% | 15.4 / 75.3 | 57 | intergenic (‑290/‑265) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 195,634 | 0 | C | T | 42.4% | 411.1 / inf | 687 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 5,224,983 | 0 | C | A | 33.3% | ‑5.5 / 10.6 | 36 | L428F (TTG→TTT) | PP_4603 | transposase |
| * | NC_002947 | 195,559 | 0 | C | A | 28.8% | 886.4 / inf | 494 | T355T (ACC→ACA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 4,355,175 | 0 | T | G | 28.0% | 352.6 / 42.5 | 207 | V112G (GTG→GGG) | yrpB | 2‑nitropropane dioxygenase |
| * | NC_002947 | 1,544,401 | 0 | C | G | 27.3% | 739.2 / 130.3 | 388 | A388G (GCG→GGG) | mdfA | multidrug MFS transporter |
| * | NC_002947 | 196,351 | 0 | C | G | 26.1% | 931.2 / inf | 477 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 5,742,449 | 0 | A | C | 25.9% | 331.4 / 16.5 | 186 | intergenic (+36/+35) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947 | 5,528,513 | 0 | T | A | 25.9% | 977.8 / 99.8 | 484 | L19Q (CTG→CAG) | PP_4860 | mannose‑6‑phosphate isomerase |
| * | NC_002947 | 196,879 | 0 | G | A | 24.9% | 316.0 / 116.5 | 182 | V795V (GTG→GTA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 4,879,291 | 0 | G | C | 24.7% | 726.9 / 84.9 | 312 | intergenic (‑372/‑28) | pucM/puuE | 5‑hydroxyisourate hydrolase/allantoinase |
| * | NC_002947 | 4,160,432 | 0 | T | G | 24.6% | 601.3 / 48.9 | 367 | L159R (CTG→CGG) | PP_3661 | membrane protein |
| * | NC_002947 | 4,355,170 | 0 | G | C | 24.4% | 442.1 / 40.2 | 217 | T110T (ACG→ACC) | yrpB | 2‑nitropropane dioxygenase |
| Marginal new junction evidence (lowest skew 10 of 549 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | 4810141 = | 53 (0.110) | 186 (0.500) | 62/226 | 8.5 | 62.1% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5990913 | 187 (0.510) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 1780108 | 197 (0.410) | 69 (0.150) | 57/282 | 12.7 | 28.8% | intergenic (+25/+81) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase |
| ? | NC_002947 | 1780171 = | 154 (0.330) | intergenic (+88/+18) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase | |||||
| * | ? | NC_002947 | = 5203537 | 279 (0.580) | 89 (0.190) | 53/290 | 14.1 | 30.0% | intergenic (‑53/‑127) | PP_4582/PP_4583 | membrane protein/putative Peptidase |
| ? | NC_002947 | 5203636 = | 141 (0.300) | intergenic (‑152/‑28) | PP_4582/PP_4583 | membrane protein/putative Peptidase | |||||
| * | ? | NC_002947 | = 5990749 | 362 (0.750) | 59 (0.130) | 45/280 | 15.5 | 16.0% | intergenic (+65/‑481) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947 | 5990941 = | 278 (0.610) | intergenic (+257/‑289) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 4810146 | 52 (0.110) | 133 (0.300) +CGGCGCTTCGCGG |
37/270 | 17.1 | 51.5% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 4947183 = | 223 (0.460) | intergenic (+576/+222) | PP_5673/flhB | D‑alanine‑‑D‑alanine ligase/flagellin export apparatus substrate specificity protein | |||||
| * | ? | NC_002947 | 1847008 = | 485 (1.000) | 41 (0.130) +48 bp |
11/200 | 23.6 | 11.2% | coding (1257/1377 nt) | pfeS‑II | histidine kinase |
| ? | NC_002947 | 2437200 = | NA (NA) | intergenic (+82/‑222) | PP_2133/PP_2134 | hypothetical protein/transposase | |||||
| * | ? | NC_002947 | 4587985 = | 263 (0.540) | 22 (0.060) | 11/220 | 25.0 | 12.1% | intergenic (+102/+115) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947 | 4588089 = | 125 (0.350) | intergenic (+206/+11) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947 | = 4585460 | 301 (0.620) | 25 (0.060) | 14/256 | 25.5 | 9.5% | intergenic (‑67/+104) | treSB/glgE | bifunctional trehalose synthase B/maltokinase/alpha‑1,4‑glucan:maltose‑1‑phosphate maltosyltransferase |
| ? | NC_002947 | = 4585521 | 214 (0.510) | intergenic (‑128/+43) | treSB/glgE | bifunctional trehalose synthase B/maltokinase/alpha‑1,4‑glucan:maltose‑1‑phosphate maltosyltransferase | |||||
| * | ? | NC_002947 | 4539515 = | NA (NA) | 60 (0.130) | 16/286 | 26.1 | 46.3% | coding (884/1533 nt) | PP_4025 | transposase |
| ? | NC_002947 | = 4628624 | 72 (0.150) | coding (848/1533 nt) | PP_4091 | transposase | |||||
| * | ? | NC_002947 | 4539479 = | NA (NA) | 61 (0.130) | 16/286 | 26.1 | NA | coding (848/1533 nt) | PP_4025 | transposase |
| ? | NC_002947 | 4539515 = | NA (NA) | coding (884/1533 nt) | PP_4025 | transposase | |||||