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 34 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 4,733,482 | 0 | C | A | 66.2% | 68.4 / 67.0 | 68 | R718L (CGC→CTC) | sucA | 2‑oxoglutarate dehydrogenase subunit E1 |
| * | NC_002947 | 1,327,121 | 0 | C | T | 52.5% | 20.5 / 155.4 | 118 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 195,634 | 0 | C | T | 47.2% | 30.3 / 135.8 | 106 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 699,722 | 0 | A | G | 43.3% | 33.8 / 75.7 | 67 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 5,947,761 | 0 | C | T | 43.0% | 33.2 / 88.5 | 80 | R238H (CGC→CAC) | rho | transcription termination factor Rho |
| * | NC_002947 | 4,138,434 | 0 | A | G | 37.8% | 51.0 / 74.3 | 74 | intergenic (‑249/‑68) | PP_3641/PP_3643 | cytosine/purine/uracil/thiamine/allantoin permease family protein/oxidoreductase |
| * | NC_002947 | 4,348,705 | 0 | A | G | 35.7% | 102.9 / 93.1 | 98 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 195,559 | 0 | C | A | 29.6% | 128.2 / 65.0 | 81 | T355T (ACC→ACA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 5,988,911 | 0 | A | . | 28.1% | 199.8 / 81.5 | 84 | intergenic (+205/‑341) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 196,327 | 0 | A | C | 27.8% | 164.4 / 72.1 | 97 | T611T (ACA→ACC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 5,988,905 | 0 | T | C | 27.5% | 126.1 / 52.7 | 80 | intergenic (+199/‑347) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 4,621,021 | 0 | A | . | 27.1% | 172.8 / 67.3 | 70 | coding (31/417 nt) | PP_5654 | phosphotriesterase |
| * | NC_002947 | 5,551,996 | 0 | T | C | 27.1% | 128.5 / 56.4 | 87 | S409P (TCA→CCA) | PP_4882 | iron ABC transporter permease |
| * | NC_002947 | 196,351 | 0 | C | G | 26.7% | 181.4 / 69.9 | 101 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 5,988,894 | 0 | C | T | 25.9% | 146.9 / 48.5 | 81 | intergenic (+188/‑358) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,988,895 | 0 | A | G | 25.9% | 136.6 / 49.1 | 81 | intergenic (+189/‑357) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,988,889 | 0 | C | A | 25.6% | 165.4 / 41.9 | 79 | intergenic (+183/‑363) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 196,306 | 0 | T | C | 25.0% | 180.3 / 55.7 | 100 | N604N (AAT→AAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 3,853,118 | 0 | T | A | 24.2% | 51.7 / 15.8 | 33 | I169N (ATT→AAT) | alkB | alpha‑ketoglutarate‑ and Fe(II)‑dependent dioxygenase |
| * | NC_002947 | 5,740,467 | 0 | T | G | 24.2% | 92.0 / 31.9 | 62 | intergenic (+32/+39) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| Marginal new junction evidence (lowest skew 10 of 561 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | 4182122 = | 34 (0.480) | 29 (0.410) | 24/280 | 3.3 | 46.0% | intergenic (‑137/‑101) | PP_3679/PP_3680 | hypothetical protein/hypothetical protein |
| ? | NC_002947 | 4625926 = | NA (NA) | intergenic (+4519/+45) | PP_5654/PP_4091 | phosphotriesterase/transposase | |||||
| * | ? | NC_002947 | = 1499458 | 29 (0.410) | 20 (0.290) | 20/276 | 4.1 | 39.8% | intergenic (+35/‑129) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| ? | NC_002947 | = 1499495 | 32 (0.460) | intergenic (+72/‑92) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein | |||||
| * | ? | NC_002947 | = 652782 | 57 (0.810) | 20 (0.330) | 15/240 | 4.5 | 45.0% | coding (1961/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947 | = 4808159 | 0 (0.000) | intergenic (‑268/‑287) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947 | = 1419549 | 32 (0.450) | 21 (0.300) | 17/274 | 4.8 | 35.8% | intergenic (‑38/+98) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein |
| ? | NC_002947 | = 1419636 | 44 (0.640) | intergenic (‑125/+11) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein | |||||
| * | ? | NC_002947 | = 4182129 | 40 (0.570) | 21 (0.300) | 16/280 | 5.2 | 34.4% | intergenic (‑144/‑94) | PP_3679/PP_3680 | hypothetical protein/hypothetical protein |
| ? | NC_002947 | 4536203 = | NA (NA) | intergenic (+730/‑85) | PP_4022/PP_4024 | hypothetical protein/transposase | |||||
| * | ? | NC_002947 | 1731163 = | 44 (0.620) | 12 (0.210) | 11/224 | 5.4 | 24.2% | intergenic (‑76/+115) | dapE/PP_1526 | succinyl‑diaminopimelate desuccinylase/beta‑(1‑3)‑glucosyl transferase |
| ? | NC_002947 | 1731255 = | 40 (0.710) | intergenic (‑168/+23) | dapE/PP_1526 | succinyl‑diaminopimelate desuccinylase/beta‑(1‑3)‑glucosyl transferase | |||||
| * | ? | NC_002947 | 1967145 = | 57 (0.810) | 11 (0.200) | 10/214 | 5.5 | 22.6% | intergenic (+15/+104) | PP_1762/yciK | hypothetical protein/putative oxidoreductase |
| ? | NC_002947 | 1967241 = | 32 (0.590) | intergenic (+111/+8) | PP_1762/yciK | hypothetical protein/putative oxidoreductase | |||||
| * | ? | NC_002947 | = 3787977 | 31 (0.470) | 15 (0.230) +CCAACTGT |
12/246 | 5.6 | 31.5% | coding (658/1392 nt) | PP_3350 | hypothetical protein |
| ? | NC_002947 | 3787978 = | 36 (0.510) | coding (657/1392 nt) | PP_3350 | hypothetical protein | |||||
| * | ? | NC_002947 | = 1419549 | 31 (0.440) | 16 (0.230) +CT |
14/276 | 5.7 | 29.9% | intergenic (‑38/+98) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein |
| ? | NC_002947 | = 1780139 | 45 (0.640) | intergenic (+98/+8) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase | |||||
| * | ? | NC_002947 | = 4073915 | NA (NA) | 14 (0.200) | 13/272 | 5.9 | 18.6% | intergenic (‑453/+171) | mdtA/PP_3586 | multidrug transporter membrane fusion protein/transposase |
| ? | NC_002947 | = 4302585 | 63 (0.890) | intergenic (+1075/‑225) | PP_3774/PP_5627 | hypothetical protein/hypothetical protein | |||||