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 32 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 5,986,841 | 0 | T | A | 74.0% | 85.3 / 27.4 | 50 | intergenic (+121/‑78) | PP_5245/kefB‑III | AraC family transcriptional regulator/glutathione‑regulated potassium/H+ antiporter |
| * | NC_002947 | 195,634 | 0 | C | T | 55.6% | ‑1.1 / 130.4 | 108 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 1,327,121 | 0 | C | T | 53.8% | 11.0 / 114.8 | 91 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 4,348,705 | 0 | A | G | 51.1% | 10.7 / 122.6 | 90 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 699,722 | 0 | A | G | 50.0% | 10.8 / 110.4 | 78 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 195,559 | 0 | C | A | 37.8% | 87.9 / 78.8 | 74 | T355T (ACC→ACA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 196,390 | 0 | T | C | 35.0% | 57.7 / 51.3 | 60 | D632D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 2,282,775 | 0 | G | C | 32.7% | 51.4 / 41.7 | 55 | intergenic (‑167/+62) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 2,282,779 | 0 | C | A | 32.7% | 44.5 / 37.7 | 52 | intergenic (‑171/+58) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 441,326 | 0 | G | . | 31.4% | 76.4 / 39.2 | 35 | coding (207/1173 nt) | bioF | 8‑amino‑7‑oxononanoate synthase |
| * | NC_002947 | 2,282,774 | 0 | G | C | 30.9% | 64.8 / 41.9 | 55 | intergenic (‑166/+63) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 196,351 | 0 | C | G | 30.8% | 103.5 / 69.3 | 78 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 2,282,770 | 0 | T | G | 27.1% | 65.7 / 38.7 | 59 | intergenic (‑162/+67) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 197,590 | 0 | T | C | 27.1% | 165.3 / 72.0 | 109 | D1032D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 196,327 | 0 | A | C | 26.2% | 141.1 / 54.9 | 84 | T611T (ACA→ACC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 5,740,467 | 0 | T | G | 25.5% | 53.0 / 29.2 | 47 | intergenic (+32/+39) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947 | 2,029,411 | 0 | G | T | 25.4% | 105.2 / 39.3 | 59 | G384V (GGG→GTG) | wbpM | polysaccharide biosynthesis protein |
| * | NC_002947 | 4,842,896 | 0 | C | . | 24.5% | 122.4 / 43.3 | 53 | intergenic (+40/‑257) | ccoP‑II/PP_4259 | cbb3‑type cytochrome c oxidase subunit/iron‑sulfur cluster‑binding protein |
| * | NC_002947 | 197,572 | 0 | G | A | 23.3% | 210.3 / 61.6 | 116 | K1026K (AAG→AAA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 196,306 | 0 | T | C | 23.2% | 169.0 / 52.4 | 95 | N604N (AAT→AAC) | PP_0168 | putative surface adhesion protein |
| Marginal new junction evidence (lowest skew 10 of 237 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | = 3951097 | 44 (0.690) | 22 (0.350) | 20/276 | 3.4 | 38.7% | intergenic (‑61/+134) | PP_3486/PP_3487 | cytochrome c/hypothetical protein |
| ? | NC_002947 | = 3951157 | 26 (0.410) | intergenic (‑121/+74) | PP_3486/PP_3487 | cytochrome c/hypothetical protein | |||||
| * | ? | NC_002947 | 5334843 = | 73 (1.150) | 17 (0.290) | 16/258 | 4.0 | 20.4% | coding (1273/2976 nt) | PP_4695 | two‑component system sensor histidine kinase |
| ? | NC_002947 | = 5334835 | 65 (1.100) | coding (1265/2976 nt) | PP_4695 | two‑component system sensor histidine kinase | |||||
| * | ? | NC_002947 | = 2051324 | 46 (0.730) | 17 (0.270) | 16/272 | 4.2 | 27.4% | coding (355/591 nt) | PP_1826 | isochorismatase family hydrolase |
| ? | NC_002947 | 3826611 = | NA (NA) | intergenic (‑566/+37) | ptxS/PP_3381 | 2‑ketogluconate utilization repressor/transposase | |||||
| * | ? | NC_002947 | = 5816871 | 40 (0.630) | 15 (0.270) | 13/242 | 4.4 | 32.0% | intergenic (+57/+72) | PP_5092/pilT | NLP/P60 protein/twitching motility protein |
| ? | NC_002947 | = 5816898 | 29 (0.530) | intergenic (+84/+45) | PP_5092/pilT | NLP/P60 protein/twitching motility protein | |||||
| * | ? | NC_002947 | = 1419549 | 32 (0.500) | 22 (0.350) | 15/272 | 4.5 | 40.2% | intergenic (‑38/+98) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein |
| ? | NC_002947 | = 1419636 | 34 (0.550) | intergenic (‑125/+11) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein | |||||
| * | ? | NC_002947 | 5477090 = | 58 (0.910) | 9 (0.200) | 9/196 | 4.6 | 17.5% | intergenic (+3/+109) | PP_4813/PP_4814 | PAP2 family protein/DedA family protein/ATP‑dependent protease La domain‑containing protein |
| ? | NC_002947 | 5477189 = | 44 (0.980) | intergenic (+102/+10) | PP_4813/PP_4814 | PAP2 family protein/DedA family protein/ATP‑dependent protease La domain‑containing protein | |||||
| * | ? | NC_002947 | 5759404 = | 43 (0.680) | 11 (0.230) | 10/214 | 4.7 | 26.5% | intergenic (+13/+143) | trmL/secB | tRNA (cytosine(34)‑2'‑O)‑methyltransferase TrmL/protein‑export protein SecB |
| ? | NC_002947 | 5759496 = | 28 (0.570) | intergenic (+105/+51) | trmL/secB | tRNA (cytosine(34)‑2'‑O)‑methyltransferase TrmL/protein‑export protein SecB | |||||
| * | ? | NC_002947 | = 1441693 | NA (NA) | 18 (0.290) | 14/272 | 4.8 | 28.6% | intergenic (+37/+395) | PP_1260/ghrB | transposase/2‑ketoaldonate reductase/hydroxypyruvate/glyoxylate reductase |
| ? | NC_002947 | = 2051324 | 46 (0.730) | coding (355/591 nt) | PP_1826 | isochorismatase family hydrolase | |||||
| * | ? | NC_002947 | 1844134 = | 42 (0.660) | 14 (0.230) | 13/268 | 5.0 | 17.8% | coding (660/2754 nt) | gacS | sensor protein GacS |
| ? | NC_002947 | = 2179376 | 89 (1.460) | intergenic (+175/+93) | PP_1931/PP_5486 | hypothetical protein/hypothetical protein | |||||
| * | ? | NC_002947 | = 1419549 | 32 (0.500) | 16 (0.260) +CT |
13/274 | 5.1 | 30.8% | intergenic (‑38/+98) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein |
| ? | NC_002947 | = 1780139 | 41 (0.650) | intergenic (+98/+8) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase | |||||