mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 72 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 4,741,273 | 1 | . | C | 67.5% | 87.1 / 46.1 | 40 | intergenic (+464/+288) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,275 | 0 | A | G | 67.5% | 41.4 / 28.4 | 40 | intergenic (+466/+286) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,298 | 1 | . | T | 57.1% | 79.3 / 62.8 | 42 | intergenic (+489/+263) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,302 | 0 | A | G | 57.1% | 18.6 / 42.5 | 42 | intergenic (+493/+259) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,305 | 0 | A | . | 57.1% | 14.0 / 79.2 | 42 | intergenic (+496/+256) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 1,327,127 | 0 | C | T | 55.3% | 9.5 / 104.9 | 85 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 4,348,749 | 0 | A | G | 47.4% | 8.1 / 102.2 | 79 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 4,842,949 | 1 | . | G | 46.7% | 63.8 / 100.3 | 45 | intergenic (+48/‑249) | ccoP‑II/PP_4259 | cbb3‑type cytochrome c oxidase subunit/iron‑sulfur cluster‑binding protein |
| * | NC_002947 | 5,988,945 | 0 | C | A | 44.8% | 93.8 / 90.5 | 87 | intergenic (+183/‑363) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,988,951 | 0 | A | G | 44.7% | 65.4 / 102.5 | 85 | intergenic (+189/‑357) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,988,950 | 0 | C | T | 44.0% | 65.7 / 96.8 | 85 | intergenic (+188/‑358) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 4,741,299 | 0 | C | T | 42.9% | 23.3 / 38.9 | 42 | intergenic (+490/+262) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,301 | 0 | A | C | 42.9% | 14.6 / 46.1 | 42 | intergenic (+492/+260) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,304 | 0 | C | G | 42.9% | 28.5 / 49.5 | 42 | intergenic (+495/+257) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 5,988,961 | 0 | T | C | 42.5% | 74.7 / 96.1 | 87 | intergenic (+199/‑347) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 4,842,941 | 0 | C | . | 41.3% | 86.7 / 71.9 | 46 | intergenic (+40/‑257) | ccoP‑II/PP_4259 | cbb3‑type cytochrome c oxidase subunit/iron‑sulfur cluster‑binding protein |
| * | NC_002947 | 195,634 | 0 | C | T | 40.0% | 83.6 / 125.1 | 120 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 699,725 | 0 | A | G | 38.9% | 36.4 / 52.9 | 54 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 5,988,967 | 0 | A | . | 36.8% | 160.3 / 102.9 | 76 | intergenic (+205/‑341) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 1,070,265 | 0 | G | C | 33.3% | 34.2 / 22.1 | 29 | intergenic (+62/+82) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| Marginal new junction evidence (lowest skew 10 of 548 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | = 4861197 | 79 (1.150) | 24 (0.430) | 16/216 | 3.3 | 29.6% | intergenic (‑103/+134) | ligA/PP_4275 | DNA ligase/cell division protein ZipA |
| ? | NC_002947 | = 4861238 | 50 (0.900) | intergenic (‑144/+93) | ligA/PP_4275 | DNA ligase/cell division protein ZipA | |||||
| * | ? | NC_002947 | = 4586100 | 41 (0.600) | 13 (0.260) | 11/190 | 3.9 | 34.1% | intergenic (+139/+78) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947 | = 4586128 | 21 (0.430) | intergenic (+167/+50) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947 | = 176399 | NA (NA) | 25 (0.380) +CGAAA |
16/256 | 4.1 | 35.6% | intergenic (+43/‑420) | PP_5SA/PP_16SB | 5S ribosomal RNA/16S ribosomal RNA |
| ? | NC_002947 | = 182013 | 47 (0.680) | intergenic (+2/+63) | PP_5SB/PP_0160 | 5S ribosomal RNA/ferrioxamine receptor | |||||
| * | ? | NC_002947 | 4647603 = | 50 (0.730) | 9 (0.190) | 9/188 | 4.5 | 25.6% | intergenic (+10/+121) | fusB/PP_4112 | elongation factor G 2/sulfate transporter |
| ? | NC_002947 | 4647711 = | 17 (0.350) | intergenic (+118/+13) | fusB/PP_4112 | elongation factor G 2/sulfate transporter | |||||
| * | ? | NC_002947 | 5743378 = | 64 (0.930) | 15 (0.230) | 13/248 | 4.7 | 19.9% | intergenic (‑155/+92) | fbp/glgP | class 1 fructose‑1,6‑bisphosphatase/glycogen phosphorylase |
| ? | NC_002947 | 5743460 = | 61 (0.950) | intergenic (‑237/+10) | fbp/glgP | class 1 fructose‑1,6‑bisphosphatase/glycogen phosphorylase | |||||
| * | ? | NC_002947 | 4340085 = | 36 (0.520) | 12 (0.230) | 9/198 | 4.8 | 33.9% | intergenic (+26/‑305) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| ? | NC_002947 | 4340169 = | 20 (0.390) | intergenic (+110/‑221) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein | |||||
| * | ? | NC_002947 | 4159113 = | 71 (1.030) | 13 (0.210) | 12/240 | 4.8 | 19.5% | intergenic (+17/‑192) | PP_3661/PP_3662 | membrane protein/hypothetical protein |
| ? | NC_002947 | 4159201 = | 43 (0.690) | intergenic (+105/‑104) | PP_3661/PP_3662 | membrane protein/hypothetical protein | |||||
| * | ? | NC_002947 | 478264 = | 63 (0.920) | 9 (0.170) | 9/206 | 5.0 | 14.3% | intergenic (+9/+101) | PP_0393/cca | 2‑amino‑4‑hydroxy‑6‑ hydroxymethyldihydropteridine pyrophosphokinase/multifunctional tRNA nucleotidyltransferase/2',3'‑cyclic phosphodiesterase/2' nucleotidase/phosphatase |
| ? | NC_002947 | 478359 = | 59 (1.110) | intergenic (+104/+6) | PP_0393/cca | 2‑amino‑4‑hydroxy‑6‑ hydroxymethyldihydropteridine pyrophosphokinase/multifunctional tRNA nucleotidyltransferase/2',3'‑cyclic phosphodiesterase/2' nucleotidase/phosphatase | |||||
| * | ? | NC_002947 | = 5538612 | 48 (0.700) | 10 (0.170) | 10/224 | 5.1 | 19.5% | intergenic (+54/+67) | PP_4871/PP_4872 | lysine decarboxylase family protein/hypothetical protein |
| ? | NC_002947 | = 5538625 | 42 (0.730) | intergenic (+67/+54) | PP_4871/PP_4872 | lysine decarboxylase family protein/hypothetical protein | |||||
| * | ? | NC_002947 | = 5453186 | 11 (0.160) | 9 (0.200) +48 bp |
6/170 | 5.2 | 27.6% | intergenic (+151/‑204) | lnt/PP_4791 | apolipoprotein N‑acyltransferase/transposase |
| ? | NC_002947 | 5545674 = | 63 (0.920) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||