mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.2 revision caddc01d3be9
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 | 1,327,127 | 0 | C | T | 71.4% | 24.8 / 23.9 | 42 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 2,282,817 | 0 | G | C | 68.4% | 11.6 / 13.3 | 19 | intergenic (‑166/+63) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 2,282,818 | 0 | G | C | 68.4% | 10.3 / 14.3 | 19 | intergenic (‑167/+62) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 2,282,822 | 0 | C | A | 68.4% | 5.4 / 14.3 | 19 | intergenic (‑171/+58) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 4,741,301 | 0 | A | C | 60.0% | 12.3 / 23.3 | 25 | intergenic (+492/+260) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,304 | 0 | C | G | 60.0% | 1.9 / 30.6 | 25 | intergenic (+495/+257) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,305 | 0 | A | C | 60.0% | 43.7 / 37.3 | 25 | intergenic (+496/+256) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,299 | 0 | C | T | 56.0% | 2.0 / 25.0 | 25 | intergenic (+490/+262) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,348,749 | 0 | A | G | 50.0% | 0.5 / 68.4 | 51 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 195,634 | 0 | C | T | 44.6% | 33.7 / 69.4 | 56 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 5,655,682 | 0 | T | G | 42.1% | 0.7 / 18.5 | 19 | intergenic (‑86/+66) | epd/tktA | D‑erythrose 4‑phosphate dehydrogenase/transketolase A |
| * | NC_002947 | 5,655,687 | 0 | C | A | 42.1% | 4.5 / 11.9 | 19 | intergenic (‑91/+61) | epd/tktA | D‑erythrose 4‑phosphate dehydrogenase/transketolase A |
| * | NC_002947 | 4,741,298 | 1 | . | T | 40.0% | 4.4 / 45.9 | 25 | intergenic (+489/+263) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,302 | 0 | A | G | 40.0% | 5.3 / 23.2 | 25 | intergenic (+493/+259) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,951,017 | 0 | T | G | 40.0% | 4.4 / 14.2 | 20 | intergenic (‑122/+35) | fliL/fliK | flagellar protein FliL/flagellar hook‑length control protein FliK |
| * | NC_002947 | 4,951,018 | 0 | C | A | 40.0% | 11.0 / 12.1 | 20 | intergenic (‑123/+34) | fliL/fliK | flagellar protein FliL/flagellar hook‑length control protein FliK |
| * | NC_002947 | 5,988,967 | 0 | A | . | 39.6% | 85.8 / 70.0 | 49 | intergenic (+205/‑341) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,453,177 | 0 | G | A | 38.9% | 0.3 / 14.8 | 18 | intergenic (+142/‑213) | lnt/PP_4791 | apolipoprotein N‑acyltransferase/transposase |
| * | NC_002947 | 5,988,961 | 0 | T | C | 38.8% | 44.4 / 45.4 | 49 | intergenic (+199/‑347) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 699,725 | 0 | A | G | 37.5% | 16.5 / 26.5 | 32 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| Marginal new junction evidence (lowest skew 10 of 113 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | = 2057866 | 54 (1.430) | 8 (0.260) | 7/222 | 2.8 | 14.5% | intergenic (+39/+89) | PP_1832/PP_1833 | oxidase/hypothetical protein |
| ? | NC_002947 | = 2057906 | 50 (1.620) | intergenic (+79/+49) | PP_1832/PP_1833 | oxidase/hypothetical protein | |||||
| * | ? | NC_002947 | 235331 = | 46 (1.220) | 7 (0.210) | 7/238 | 3.0 | 15.3% | intergenic (+28/+97) | PP_0183/argH | glutathione S‑transferase/argininosuccinate lyase |
| ? | NC_002947 | 235390 = | 37 (1.110) | intergenic (+87/+38) | PP_0183/argH | glutathione S‑transferase/argininosuccinate lyase | |||||
| * | ? | NC_002947 | 5038212 = | NA (NA) | 8 (0.210) | 8/270 | 3.1 | NA | coding (1256/1536 nt) | PP_4443 | transposase |
| ? | NC_002947 | 5038234 = | NA (NA) | coding (1278/1536 nt) | PP_4443 | transposase | |||||
| * | ? | NC_002947 | = 295713 | 90 (2.390) | 8 (0.240) | 7/242 | 3.1 | 9.0% | intergenic (+60/+82) | PP_0241/PP_0242 | transporter/TetR family transcriptional regulator |
| ? | NC_002947 | = 295744 | 82 (2.430) | intergenic (+91/+51) | PP_0241/PP_0242 | transporter/TetR family transcriptional regulator | |||||
| * | ? | NC_002947 | = 2100025 | 43 (1.140) | 9 (0.290) | 6/224 | 3.2 | 22.1% | intergenic (‑93/‑112) | PP_1875/PP_1876 | two‑component system sensor histidine kinase/response regulator/AAA family ATP/GTP‑binding protein |
| ? | NC_002947 | = 2100074 | 28 (0.900) | intergenic (‑142/‑63) | PP_1875/PP_1876 | two‑component system sensor histidine kinase/response regulator/AAA family ATP/GTP‑binding protein | |||||
| * | ? | NC_002947 | = 1970782 | 34 (0.900) | 7 (0.220) | 6/230 | 3.2 | 18.7% | intergenic (+33/‑233) | mtnA/PP_mr25 | methylthioribose‑1‑phosphate isomerase/gyrA regulatory region |
| ? | NC_002947 | = 1970844 | 32 (1.000) | intergenic (+95/‑171) | mtnA/PP_mr25 | methylthioribose‑1‑phosphate isomerase/gyrA regulatory region | |||||
| * | ? | NC_002947 | = 1799915 | 52 (1.380) | 6 (0.190) | 6/224 | 3.2 | 12.6% | intergenic (+43/‑144) | rnhB/dnaEA | ribonuclease HII/DNA polymerase III subunit alpha |
| ? | NC_002947 | = 1799957 | 40 (1.280) | intergenic (+85/‑102) | rnhB/dnaEA | ribonuclease HII/DNA polymerase III subunit alpha | |||||
| * | ? | NC_002947 | 2048837 = | 42 (1.110) | 8 (0.240) | 6/236 | 3.3 | 18.7% | intergenic (+33/+106) | PP_1821/PP_1822 | glutathione S‑transferase family protein/hypothetical protein |
| ? | NC_002947 | 2048928 = | 33 (1.000) | intergenic (+124/+15) | PP_1821/PP_1822 | glutathione S‑transferase family protein/hypothetical protein | |||||
| * | ? | NC_002947 | 5537079 = | 36 (0.960) | 5 (0.170) | 5/216 | 3.4 | 13.2% | intergenic (+8/+95) | nadE/PP_4870 | NH(3)‑dependent NAD(+) synthetase/azurin |
| ? | NC_002947 | 5537155 = | 37 (1.230) | intergenic (+84/+19) | nadE/PP_4870 | NH(3)‑dependent NAD(+) synthetase/azurin | |||||
| * | ? | NC_002947 | 5734086 = | 45 (1.190) | 6 (0.170) | 6/246 | 3.5 | 12.5% | intergenic (‑56/+101) | proY/hutH | proline (histidine) APC transporter/histidine ammonia‑lyase |
| ? | NC_002947 | 5734165 = | 43 (1.250) | intergenic (‑135/+22) | proY/hutH | proline (histidine) APC transporter/histidine ammonia‑lyase | |||||