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 71 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 | 68.3% | 35.5 / 28.7 | 41 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 4,741,273 | 1 | . | C | 64.3% | 25.7 / 14.0 | 14 | intergenic (+464/+288) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,298 | 1 | . | T | 62.5% | 47.7 / 29.3 | 24 | intergenic (+489/+263) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,302 | 0 | A | G | 62.5% | 18.3 / 17.5 | 24 | intergenic (+493/+259) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,305 | 0 | A | . | 62.5% | 17.7 / 36.8 | 24 | intergenic (+496/+256) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 195,634 | 0 | C | T | 50.0% | ‑0.2 / 74.4 | 52 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 5,988,961 | 0 | T | C | 49.1% | 33.1 / 73.4 | 58 | intergenic (+199/‑347) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 4,348,749 | 0 | A | G | 49.1% | 0.2 / 73.8 | 55 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 5,988,967 | 0 | A | . | 49.0% | 84.2 / 96.0 | 53 | intergenic (+205/‑341) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,988,945 | 0 | C | A | 43.9% | 66.7 / 61.1 | 57 | intergenic (+183/‑363) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,988,950 | 0 | C | T | 43.9% | 53.0 / 66.4 | 57 | intergenic (+188/‑358) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,988,951 | 0 | A | G | 43.9% | 52.5 / 63.3 | 57 | intergenic (+189/‑357) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 1,327,127 | 0 | C | T | 40.0% | 30.4 / 46.9 | 45 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 4,741,299 | 0 | C | T | 37.5% | 16.8 / 18.2 | 24 | intergenic (+490/+262) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,301 | 0 | A | C | 37.5% | 18.0 / 18.3 | 24 | intergenic (+492/+260) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,304 | 0 | C | G | 37.5% | 26.5 / 17.7 | 24 | intergenic (+495/+257) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 5,988,904 | 0 | C | T | 35.2% | 85.7 / 43.8 | 54 | intergenic (+142/‑404) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,988,906 | 0 | C | T | 34.5% | 92.8 / 44.6 | 55 | intergenic (+144/‑402) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 4,842,949 | 1 | . | G | 34.4% | 30.7 / 47.8 | 32 | intergenic (+48/‑249) | ccoP‑II/PP_4259 | cbb3‑type cytochrome c oxidase subunit/iron‑sulfur cluster‑binding protein |
| * | NC_002947 | 5,988,865 | 0 | G | A | 34.3% | 114.9 / 59.0 | 70 | intergenic (+103/‑443) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| Marginal new junction evidence (lowest skew 10 of 191 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | 661526 = | 63 (1.650) | 8 (0.240) | 8/246 | 2.9 | 13.5% | intergenic (+33/+94) | PP_0568/PP_0569 | hypothetical protein/MATE efflux family protein |
| ? | NC_002947 | 661591 = | 47 (1.390) | intergenic (+98/+29) | PP_0568/PP_0569 | hypothetical protein/MATE efflux family protein | |||||
| * | ? | NC_002947 | = 353089 | 57 (1.490) | 8 (0.260) | 7/220 | 2.9 | 13.9% | intergenic (+53/+65) | hisF/cbcV | imidazole glycerol phosphate synthase subunit HisF/choline/betaine/carnitine ABC transporter ATP binding protein |
| ? | NC_002947 | = 353103 | 54 (1.790) | intergenic (+67/+51) | hisF/cbcV | imidazole glycerol phosphate synthase subunit HisF/choline/betaine/carnitine ABC transporter ATP binding protein | |||||
| * | ? | NC_002947 | 4896423 = | 41 (1.070) | 9 (0.280) | 7/236 | 3.1 | 20.7% | intergenic (+11/‑197) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein |
| ? | NC_002947 | 4896512 = | 34 (1.050) | intergenic (+100/‑108) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein | |||||
| * | ? | NC_002947 | 4564007 = | 36 (0.940) | 8 (0.220) | 8/262 | 3.2 | 19.1% | intergenic (‑103/‑795) | vgrG‑III/glgA | type VI secretion system protein/glycogen synthase |
| ? | NC_002947 | 4564038 = | 34 (0.940) | intergenic (‑134/‑764) | vgrG‑III/glgA | type VI secretion system protein/glycogen synthase | |||||
| * | ? | NC_002947 | 2414865 = | 38 (0.990) | 8 (0.220) | 8/262 | 3.2 | 15.7% | coding (20/198 nt) | PP_2115 | hypothetical protein |
| ? | NC_002947 | = 4022407 | 50 (1.390) | intergenic (‑58/+610) | PP_3547/emrB | NAD(P)‑binding oxidoreductase/multidrug transporter permease | |||||
| * | ? | NC_002947 | = 2078299 | 33 (0.860) | 7 (0.210) | 7/244 | 3.2 | 17.5% | intergenic (+41/+74) | PP_1853/PP_1854 | LysR family transcriptional regulator/hypothetical protein |
| ? | NC_002947 | = 2078346 | 37 (1.100) | intergenic (+88/+27) | PP_1853/PP_1854 | LysR family transcriptional regulator/hypothetical protein | |||||
| * | ? | NC_002947 | 1731205 = | 40 (1.050) | 6 (0.200) | 6/222 | 3.2 | 12.9% | intergenic (‑76/+115) | dapE/PP_1526 | succinyl‑diaminopimelate desuccinylase/beta‑(1‑3)‑glucosyl transferase |
| ? | NC_002947 | 1731297 = | 49 (1.610) | intergenic (‑168/+23) | dapE/PP_1526 | succinyl‑diaminopimelate desuccinylase/beta‑(1‑3)‑glucosyl transferase | |||||
| * | ? | NC_002947 | 5743388 = | 54 (1.410) | 9 (0.240) | 8/272 | 3.3 | 14.4% | intergenic (‑165/+82) | fbp/glgP | class 1 fructose‑1,6‑bisphosphatase/glycogen phosphorylase |
| ? | NC_002947 | 5743450 = | 54 (1.440) | intergenic (‑227/+20) | fbp/glgP | class 1 fructose‑1,6‑bisphosphatase/glycogen phosphorylase | |||||
| * | ? | NC_002947 | = 4700803 | 41 (1.070) | 9 (0.260) | 7/250 | 3.3 | 21.5% | intergenic (‑70/+80) | kdpD/kdpC | sensor protein/potassium‑transporting ATPase subunit C |
| ? | NC_002947 | = 4700847 | 29 (0.840) | intergenic (‑114/+36) | kdpD/kdpC | sensor protein/potassium‑transporting ATPase subunit C | |||||
| * | ? | NC_002947 | = 4647641 | 18 (0.470) | 7 (0.250) | 5/200 | 3.3 | 25.9% | intergenic (+48/+83) | fusB/PP_4112 | elongation factor G 2/sulfate transporter |
| ? | NC_002947 | = 4647671 | 27 (0.980) | intergenic (+78/+53) | fusB/PP_4112 | elongation factor G 2/sulfate transporter | |||||