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 84 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 699,725 | 0 | A | G | 58.9% | 29.4 / 81.8 | 74 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 4,741,298 | 1 | . | T | 56.4% | 69.8 / 60.3 | 39 | intergenic (+489/+263) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,302 | 0 | A | G | 56.4% | 16.3 / 38.9 | 39 | intergenic (+493/+259) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,305 | 0 | A | . | 56.4% | 10.4 / 75.1 | 39 | intergenic (+496/+256) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 1,327,127 | 0 | C | T | 54.5% | ‑0.9 / 104.0 | 88 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 4,348,749 | 0 | A | G | 47.4% | 16.2 / 97.3 | 78 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 5,988,945 | 0 | C | A | 46.5% | 102.8 / 112.1 | 101 | intergenic (+183/‑363) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,988,950 | 0 | C | T | 43.8% | 78.3 / 112.2 | 97 | intergenic (+188/‑358) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 4,741,299 | 0 | C | T | 43.6% | 20.5 / 34.0 | 39 | intergenic (+490/+262) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,301 | 0 | A | C | 43.6% | 16.6 / 38.1 | 39 | intergenic (+492/+260) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 5,988,967 | 0 | A | . | 43.3% | 165.6 / 148.0 | 90 | intergenic (+205/‑341) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,988,951 | 0 | A | G | 43.3% | 78.9 / 108.2 | 97 | intergenic (+189/‑357) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,988,961 | 0 | T | C | 42.3% | 85.8 / 96.5 | 98 | intergenic (+199/‑347) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 4,741,304 | 0 | C | G | 42.1% | 30.7 / 39.0 | 39 | intergenic (+495/+257) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 195,634 | 0 | C | T | 41.4% | 89.6 / 129.7 | 117 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 5,173,295 | 0 | G | C | 34.8% | 55.4 / 47.0 | 47 | intergenic (‑288/+44) | fadD‑I/fadD‑II | long‑chain‑fatty acid‑‑CoA ligase/long‑chain‑fatty acid‑‑CoA ligase |
| * | NC_002947 | 5,173,296 | 0 | G | C | 34.0% | 56.9 / 41.9 | 47 | intergenic (‑289/+43) | fadD‑I/fadD‑II | long‑chain‑fatty acid‑‑CoA ligase/long‑chain‑fatty acid‑‑CoA ligase |
| * | NC_002947 | 5,173,292 | 0 | T | C | 33.3% | 54.3 / 37.1 | 49 | intergenic (‑285/+47) | fadD‑I/fadD‑II | long‑chain‑fatty acid‑‑CoA ligase/long‑chain‑fatty acid‑‑CoA ligase |
| * | NC_002947 | 5,173,299 | 0 | G | A | 33.3% | 52.4 / 34.0 | 48 | intergenic (‑292/+40) | fadD‑I/fadD‑II | long‑chain‑fatty acid‑‑CoA ligase/long‑chain‑fatty acid‑‑CoA ligase |
| * | NC_002947 | 5,988,900 | 0 | C | G | 33.0% | 212.8 / 97.1 | 103 | intergenic (+138/‑408) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| Marginal new junction evidence (lowest skew 10 of 410 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | 1114875 = | 41 (0.730) | 14 (0.310) | 12/216 | 3.2 | 28.8% | intergenic (‑64/+115) | rlmF/valS | ribosomal RNA large subunit methyltransferase F/valine‑‑tRNA ligase |
| ? | NC_002947 | 1114951 = | 36 (0.790) | intergenic (‑140/+39) | rlmF/valS | ribosomal RNA large subunit methyltransferase F/valine‑‑tRNA ligase | |||||
| * | ? | NC_002947 | = 5201663 | 34 (0.610) | 10 (0.250) | 9/192 | 3.5 | 28.0% | intergenic (‑101/‑79) | PP_4582/PP_4583 | membrane protein/putative Peptidase |
| ? | NC_002947 | = 5201684 | 27 (0.670) | intergenic (‑122/‑58) | PP_4582/PP_4583 | membrane protein/putative Peptidase | |||||
| * | ? | NC_002947 | = 2103083 | 54 (0.960) | 8 (0.210) +41 bp |
8/184 | 3.6 | 18.8% | noncoding (76/76 nt) | PP_t23 | tRNA‑Gly |
| ? | NC_002947 | 4632531 = | 46 (0.820) | intergenic (+90/+69) | PP_4096/PP_t59 | hypothetical protein/tRNA‑Gly | |||||
| * | ? | NC_002947 | = 2102836 | 68 (1.210) | 8 (0.210) +41 bp |
8/184 | 3.6 | 16.9% | noncoding (76/76 nt) | PP_t21 | tRNA‑Gly |
| ? | NC_002947 | 4632531 = | 46 (0.820) | intergenic (+90/+69) | PP_4096/PP_t59 | hypothetical protein/tRNA‑Gly | |||||
| * | ? | NC_002947 | 1932621 = | 46 (0.820) | 10 (0.230) | 10/210 | 3.6 | 21.9% | intergenic (‑46/+105) | rluA/minE | bifunctional tRNA pseudouridine(32) synthase TrmQ/ribosomal large subunit pseudouridine synthase RluA/cell division topological specificity factor |
| ? | NC_002947 | 1932693 = | 35 (0.790) | intergenic (‑118/+33) | rluA/minE | bifunctional tRNA pseudouridine(32) synthase TrmQ/ribosomal large subunit pseudouridine synthase RluA/cell division topological specificity factor | |||||
| * | ? | NC_002947 | = 4861197 | 65 (1.160) | 12 (0.260) | 10/216 | 3.7 | 18.9% | intergenic (‑103/+134) | ligA/PP_4275 | DNA ligase/cell division protein ZipA |
| ? | NC_002947 | = 4861238 | 50 (1.100) | intergenic (‑144/+93) | ligA/PP_4275 | DNA ligase/cell division protein ZipA | |||||
| * | ? | NC_002947 | = 2429960 | 21 (0.370) | 9 (0.210) | 9/200 | 3.7 | 38.5% | intergenic (+47/+66) | PP_2129/PP_2130 | hypothetical protein/lytic transglycosylase |
| ? | NC_002947 | = 2429975 | 13 (0.310) | intergenic (+62/+51) | PP_2129/PP_2130 | hypothetical protein/lytic transglycosylase | |||||
| * | ? | NC_002947 | 358055 = | 41 (0.730) | 12 (0.280) | 9/200 | 3.7 | 33.9% | intergenic (+20/‑110) | tdcG‑I/PP_5441 | L‑serine dehydratase/hypothetical protein |
| ? | NC_002947 | 358133 = | 16 (0.380) | intergenic (+98/‑32) | tdcG‑I/PP_5441 | L‑serine dehydratase/hypothetical protein | |||||
| * | ? | NC_002947 | = 5506637 | 65 (1.160) | 14 (0.320) | 9/208 | 3.8 | 25.5% | intergenic (+48/‑151) | PP_4839/cycA | iron‑regulated membrane protein/D‑alanine/beta‑alanine/D‑serine/glycine permease |
| ? | NC_002947 | = 5506650 | 31 (0.710) | intergenic (+61/‑138) | PP_4839/cycA | iron‑regulated membrane protein/D‑alanine/beta‑alanine/D‑serine/glycine permease | |||||
| * | ? | NC_002947 | 5201627 = | 30 (0.530) | 10 (0.250) | 8/192 | 3.8 | 29.1% | intergenic (‑65/‑115) | PP_4582/PP_4583 | membrane protein/putative Peptidase |
| ? | NC_002947 | 5201722 = | 27 (0.670) | intergenic (‑160/‑20) | PP_4582/PP_4583 | membrane protein/putative Peptidase | |||||