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 59 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 4,741,298 | 1 | . | T | 58.8% | 68.1 / 52.3 | 34 | intergenic (+489/+263) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,302 | 0 | A | G | 58.8% | 20.8 / 30.0 | 34 | intergenic (+493/+259) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,305 | 0 | A | . | 58.8% | 17.7 / 60.4 | 34 | intergenic (+496/+256) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 2,282,822 | 0 | C | A | 57.1% | ‑2.8 / 21.7 | 21 | intergenic (‑171/+58) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 1,327,127 | 0 | C | T | 56.8% | ‑3.5 / 35.9 | 37 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 2,282,813 | 0 | T | G | 56.0% | ‑6.6 / 22.9 | 25 | intergenic (‑162/+67) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 2,282,817 | 0 | G | C | 54.5% | 7.8 / 30.4 | 22 | intergenic (‑166/+63) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 2,282,818 | 0 | G | C | 54.5% | 6.8 / 31.1 | 22 | intergenic (‑167/+62) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 699,725 | 0 | A | G | 47.1% | ‑1.5 / 38.6 | 34 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 4,348,749 | 0 | A | G | 43.6% | 25.7 / 58.7 | 55 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 5,988,961 | 0 | T | C | 41.9% | 41.3 / 41.7 | 44 | intergenic (+199/‑347) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 4,741,299 | 0 | C | T | 41.2% | 18.9 / 31.8 | 34 | intergenic (+490/+262) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,301 | 0 | A | C | 41.2% | 18.4 / 34.0 | 34 | intergenic (+492/+260) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,304 | 0 | C | G | 41.2% | 32.7 / 31.5 | 34 | intergenic (+495/+257) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 5,988,950 | 0 | C | T | 40.9% | 55.3 / 42.9 | 44 | intergenic (+188/‑358) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,655,682 | 0 | T | G | 40.0% | 15.9 / 23.8 | 25 | intergenic (‑86/+66) | epd/tktA | D‑erythrose 4‑phosphate dehydrogenase/transketolase A |
| * | NC_002947 | 5,988,951 | 0 | A | G | 39.5% | 58.0 / 41.7 | 44 | intergenic (+189/‑357) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,988,945 | 0 | C | A | 38.0% | 83.3 / 41.8 | 50 | intergenic (+183/‑363) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,988,967 | 0 | A | . | 37.8% | 89.4 / 61.6 | 45 | intergenic (+205/‑341) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,655,687 | 0 | C | A | 37.0% | 30.0 / 22.4 | 27 | intergenic (‑91/+61) | epd/tktA | D‑erythrose 4‑phosphate dehydrogenase/transketolase A |
| Marginal new junction evidence (lowest skew 10 of 56 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | 3968936 = | 10 (0.300) | 9 (0.300) | 6/246 | 3.0 | 42.8% | coding (1020/1179 nt) | PP_3498 | transposase |
| ? | NC_002947 | 3968992 = | 15 (0.500) | coding (1076/1179 nt) | PP_3498 | transposase | |||||
| * | ? | NC_002947 | 401317 = | 9 (0.270) | 9 (0.300) | 6/246 | 3.0 | 43.8% | coding (900/1059 nt) | PP_0334 | transposase |
| ? | NC_002947 | 3968992 = | 15 (0.500) | coding (1076/1179 nt) | PP_3498 | transposase | |||||
| * | ? | NC_002947 | = 1499465 | 29 (0.870) | 5 (0.180) | 5/226 | 3.1 | 17.5% | intergenic (+35/‑131) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| ? | NC_002947 | = 1499502 | 23 (0.830) | intergenic (+72/‑94) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein | |||||
| * | ? | NC_002947 | = 4150058 | 40 (1.200) | 6 (0.180) | 6/268 | 3.3 | 13.6% | intergenic (+13/‑384) | PP_3654/PP_3655 | leucine‑responsive regulatory protein/cytosine/purine/uracil/thiamine/allantoin permease family protein |
| ? | NC_002947 | = 4150143 | 37 (1.130) | intergenic (+98/‑299) | PP_3654/PP_3655 | leucine‑responsive regulatory protein/cytosine/purine/uracil/thiamine/allantoin permease family protein | |||||
| * | ? | NC_002947 | = 1731232 | 15 (0.450) | 4 (0.150) | 4/216 | 3.3 | 24.3% | intergenic (‑103/+88) | dapE/PP_1526 | succinyl‑diaminopimelate desuccinylase/beta‑(1‑3)‑glucosyl transferase |
| ? | NC_002947 | = 1731268 | 13 (0.490) | intergenic (‑139/+52) | dapE/PP_1526 | succinyl‑diaminopimelate desuccinylase/beta‑(1‑3)‑glucosyl transferase | |||||
| * | ? | NC_002947 | 413997 = | 28 (0.840) | 4 (0.150) | 4/216 | 3.3 | 17.0% | intergenic (+14/‑189) | glnE/waaF | glutamate‑ammonia‑ligase adenylyltransferase/ADP‑heptose:LPS heptosyltransferase II |
| ? | NC_002947 | 414083 = | 17 (0.640) | intergenic (+100/‑103) | glnE/waaF | glutamate‑ammonia‑ligase adenylyltransferase/ADP‑heptose:LPS heptosyltransferase II | |||||
| * | ? | NC_002947 | = 5845273 | 45 (1.350) | 5 (0.160) | 5/262 | 3.5 | 10.6% | coding (128/486 nt) | coaD | phosphopantetheine adenylyltransferase |
| ? | NC_002947 | = 5845293 | 41 (1.280) | coding (148/486 nt) | coaD | phosphopantetheine adenylyltransferase | |||||
| * | ? | NC_002947 | 3426291 = | 37 (1.110) | 5 (0.160) | 5/256 | 3.5 | 13.4% | coding (197/2037 nt) | PP_3042 | terminase large subunit |
| ? | NC_002947 | 3426317 = | 30 (0.960) | coding (223/2037 nt) | PP_3042 | terminase large subunit | |||||
| * | ? | NC_002947 | 874287 = | 48 (1.440) | 4 (0.140) | 4/228 | 3.5 | 8.7% | intergenic (+21/‑138) | PP_0758/PP_0759 | hypothetical protein/hypothetical protein |
| ? | NC_002947 | 874351 = | 44 (1.580) | intergenic (+85/‑74) | PP_0758/PP_0759 | hypothetical protein/hypothetical protein | |||||
| * | ? | NC_002947 | = 2730281 | 34 (1.020) | 5 (0.150) | 5/264 | 3.6 | 12.8% | coding (685/1044 nt) | PP_2392 | MFS transporter |
| ? | NC_002947 | = 2730291 | 35 (1.080) | coding (695/1044 nt) | PP_2392 | MFS transporter | |||||