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 34 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 1,327,121 | 0 | C | T | 57.5% | ‑4.8 / 156.4 | 135 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 195,634 | 0 | C | T | 51.9% | ‑3.9 / 176.5 | 136 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 4,353,192 | 0 | C | A | 51.8% | 5.2 / 20.6 | 30 | F106L (TTC→TTA) | yrpB | 2‑nitropropane dioxygenase |
| * | NC_002947 | 699,722 | 0 | A | G | 49.4% | 3.7 / 125.7 | 89 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 195,559 | 0 | C | A | 40.8% | 72.0 / 77.3 | 71 | T355T (ACC→ACA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 4,348,705 | 0 | A | G | 40.6% | 95.0 / 137.8 | 123 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 5,988,905 | 0 | T | C | 34.8% | 69.6 / 56.6 | 66 | intergenic (+199/‑347) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,988,911 | 0 | A | . | 34.8% | 140.5 / 85.5 | 66 | intergenic (+205/‑341) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 196,390 | 0 | T | C | 34.5% | 88.9 / 74.0 | 87 | D632D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 196,351 | 0 | C | G | 31.8% | 134.4 / 100.1 | 110 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 5,988,894 | 0 | C | T | 30.3% | 98.4 / 46.6 | 66 | intergenic (+188/‑358) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,988,895 | 0 | A | G | 30.3% | 94.4 / 49.1 | 66 | intergenic (+189/‑357) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 196,327 | 0 | A | C | 29.7% | 161.8 / 100.1 | 118 | T611T (ACA→ACC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 445,103 | 0 | C | A | 28.9% | 53.0 / 18.0 | 38 | intergenic (+76/‑212) | PP_0367/PP_0368 | hypothetical protein/acyl‑CoA dehydrogenase |
| * | NC_002947 | 5,988,889 | 0 | C | A | 28.4% | 127.1 / 36.9 | 67 | intergenic (+183/‑363) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 196,306 | 0 | T | C | 27.8% | 189.8 / 88.0 | 126 | N604N (AAT→AAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 1,712,080 | 0 | A | T | 26.7% | 66.6 / 16.1 | 46 | intergenic (+71/‑187) | ppc/adk | phosphoenolpyruvate carboxylase/adenylate kinase |
| * | NC_002947 | 4,340,089 | 0 | G | C | 25.5% | 91.9 / 20.3 | 50 | intergenic (+74/‑257) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,340,081 | 0 | A | G | 25.0% | 84.8 / 23.3 | 48 | intergenic (+66/‑265) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 1,703,250 | 0 | G | C | 24.6% | 113.0 / 35.9 | 69 | intergenic (+99/‑68) | lysS/PP_1497 | lysine‑‑tRNA ligase/TetR family transcriptional regulator |
| Marginal new junction evidence (lowest skew 10 of 511 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | = 4586029 | 14 (0.200) | 24 (0.370) | 21/262 | 3.4 | 52.2% | intergenic (+112/+103) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947 | = 4586109 | 31 (0.480) | intergenic (+192/+23) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947 | 4896378 = | 63 (0.910) | 13 (0.220) | 13/242 | 4.9 | 20.7% | intergenic (+11/‑197) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein |
| ? | NC_002947 | 4896467 = | 46 (0.780) | intergenic (+100/‑108) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein | |||||
| * | ? | NC_002947 | = 5288423 | 59 (0.850) | 10 (0.180) | 8/224 | 6.3 | 18.3% | intergenic (‑104/+80) | PP_4660/mdaB | LysR family transcriptional regulator/drug activity modulator B |
| ? | NC_002947 | = 5288457 | 43 (0.780) | intergenic (‑138/+46) | PP_4660/mdaB | LysR family transcriptional regulator/drug activity modulator B | |||||
| * | ? | NC_002947 | 5759404 = | 46 (0.660) | 8 (0.150) | 7/220 | 6.7 | 18.7% | intergenic (+13/+143) | trmL/secB | tRNA (cytosine(34)‑2'‑O)‑methyltransferase TrmL/protein‑export protein SecB |
| ? | NC_002947 | 5759496 = | 34 (0.630) | intergenic (+105/+51) | trmL/secB | tRNA (cytosine(34)‑2'‑O)‑methyltransferase TrmL/protein‑export protein SecB | |||||
| * | ? | NC_002947 | = 4647595 | 43 (0.620) | 6 (0.120) | 6/206 | 6.8 | 15.6% | intergenic (+48/+83) | fusB/PP_4112 | elongation factor G 2/sulfate transporter |
| ? | NC_002947 | = 4647625 | 34 (0.670) | intergenic (+78/+53) | fusB/PP_4112 | elongation factor G 2/sulfate transporter | |||||
| * | ? | NC_002947 | = 1499458 | 33 (0.470) | 10 (0.150) | 10/280 | 6.9 | 24.5% | intergenic (+35/‑129) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| ? | NC_002947 | = 1499495 | 29 (0.420) | intergenic (+72/‑92) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein | |||||
| * | ? | NC_002947 | 742915 = | NA (NA) | 13 (0.200) | 9/272 | 7.2 | NA | coding (1016/1422 nt) | PP_0635 | group II intron‑encoding maturase |
| ? | NC_002947 | 742945 = | NA (NA) | coding (1046/1422 nt) | PP_0635 | group II intron‑encoding maturase | |||||
| * | ? | NC_002947 | 6000903 = | 59 (0.850) | 7 (0.130) | 6/224 | 7.3 | 15.0% | intergenic (+10/+99) | PP_5256/amaA | cyclic nucleotide‑binding protein/L‑pipecolate oxidase |
| ? | NC_002947 | 6000997 = | 33 (0.600) | intergenic (+104/+5) | PP_5256/amaA | cyclic nucleotide‑binding protein/L‑pipecolate oxidase | |||||
| * | ? | NC_002947 | = 4808179 | 0 (0.000) | 13 (0.200) | 8/260 | 7.3 | 42.6% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 5988765 = | 35 (0.550) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | 4647557 = | 54 (0.780) | 6 (0.120) | 5/206 | 7.3 | 14.1% | intergenic (+10/+121) | fusB/PP_4112 | elongation factor G 2/sulfate transporter |
| ? | NC_002947 | 4647665 = | 34 (0.670) | intergenic (+118/+13) | fusB/PP_4112 | elongation factor G 2/sulfate transporter | |||||