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 34 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 699,722 | 0 | A | G | 59.5% | 31.9 / 77.9 | 75 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 1,327,121 | 0 | C | T | 51.6% | 36.6 / 169.6 | 122 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 195,634 | 0 | C | T | 49.6% | 35.4 / 177.2 | 127 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 4,348,705 | 0 | A | G | 46.5% | 43.8 / 129.9 | 99 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 195,559 | 0 | C | A | 34.1% | 122.9 / 87.2 | 91 | T355T (ACC→ACA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 5,988,905 | 0 | T | C | 33.7% | 108.0 / 82.8 | 98 | intergenic (+199/‑347) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,988,911 | 0 | A | . | 33.0% | 226.7 / 124.0 | 100 | intergenic (+205/‑341) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,988,894 | 0 | C | T | 30.5% | 129.8 / 72.8 | 95 | intergenic (+188/‑358) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,988,895 | 0 | A | G | 30.5% | 124.2 / 73.6 | 95 | intergenic (+189/‑357) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 3,578,433 | 0 | G | T | 29.5% | 97.7 / 23.2 | 61 | intergenic (+110/‑214) | PP_3158/PP_5589 | hypothetical protein/rhs repeat‑associated core domain‑containing protein |
| * | NC_002947 | 4,842,904 | 1 | . | G | 25.9% | 167.1 / 90.2 | 81 | intergenic (+48/‑249) | ccoP‑II/PP_4259 | cbb3‑type cytochrome c oxidase subunit/iron‑sulfur cluster‑binding protein |
| * | NC_002947 | 4,842,896 | 0 | C | . | 24.7% | 191.3 / 65.4 | 79 | intergenic (+40/‑257) | ccoP‑II/PP_4259 | cbb3‑type cytochrome c oxidase subunit/iron‑sulfur cluster‑binding protein |
| * | NC_002947 | 1,703,252 | 0 | C | T | 24.3% | 119.6 / 39.1 | 74 | intergenic (+101/‑66) | lysS/PP_1497 | lysine‑‑tRNA ligase/TetR family transcriptional regulator |
| * | NC_002947 | 5,988,889 | 0 | C | A | 23.9% | 186.2 / 53.3 | 92 | intergenic (+183/‑363) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 1,544,494 | 0 | C | G | 23.4% | 93.7 / 24.4 | 47 | intergenic (+53/+61) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,703,248 | 0 | A | G | 22.5% | 127.8 / 32.5 | 76 | intergenic (+97/‑70) | lysS/PP_1497 | lysine‑‑tRNA ligase/TetR family transcriptional regulator |
| * | NC_002947 | 1,921,550 | 0 | T | A | 22.4% | 81.6 / 21.8 | 49 | intergenic (+25/+36) | PP_1720/PP_1721 | alcohol dehydrogenase/phosphoserine phosphatase |
| * | NC_002947 | 337,819 | 0 | A | C | 22.2% | 119.3 / 29.5 | 64 | intergenic (‑69/+60) | PP_0279/PP_0280 | hypothetical protein/amino acid ABC transporter permease |
| * | NC_002947 | 3,466,841 | 0 | T | G | 22.0% | 106.6 / 11.3 | 61 | intergenic (‑16/+108) | PP_3081/PP_5560 | hypothetical protein/hypothetical protein |
| * | NC_002947 | 196,351 | 0 | C | G | 22.0% | 166.5 / 53.4 | 92 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
| Marginal new junction evidence (lowest skew 10 of 724 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | = 5453138 | 6 (0.090) | 10 (0.220) +48 bp |
9/178 | 4.9 | 33.9% | intergenic (+151/‑204) | lnt/PP_4791 | apolipoprotein N‑acyltransferase/transposase |
| ? | NC_002947 | 5545626 = | 54 (0.770) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||
| * | ? | NC_002947 | 5224500 = | 5 (0.070) | 10 (0.220) +48 bp |
9/178 | 4.9 | 34.3% | intergenic (‑204/+175) | PP_4603/PP_4604 | transposase/DMT superfamily permease |
| ? | NC_002947 | 5545626 = | 54 (0.770) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||
| * | ? | NC_002947 | 4075618 = | 6 (0.090) | 10 (0.220) +48 bp |
9/178 | 4.9 | 33.9% | intergenic (‑204/+237) | PP_3586/tpx | transposase/2‑Cys peroxiredoxin |
| ? | NC_002947 | 5545626 = | 54 (0.770) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||
| * | ? | NC_002947 | 3828180 = | 5 (0.070) | 10 (0.220) +48 bp |
9/178 | 4.9 | 34.3% | intergenic (‑204/+155) | PP_3381/PP_3382 | transposase/gluconate 2‑dehydrogenase cytochrome c subunit |
| ? | NC_002947 | 5545626 = | 54 (0.770) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||
| * | ? | NC_002947 | 2939258 = | 10 (0.140) | 10 (0.220) +48 bp |
9/178 | 4.9 | 32.5% | intergenic (‑204/+236) | PP_2570/PP_2572 | transposase/hypothetical protein |
| ? | NC_002947 | 5545626 = | 54 (0.770) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||
| * | ? | NC_002947 | = 1440124 | 4 (0.060) | 10 (0.220) +48 bp |
9/178 | 4.9 | 34.7% | intergenic (‑455/‑204) | yveA/PP_1260 | aspartate‑proton symporter/transposase |
| ? | NC_002947 | 5545626 = | 54 (0.770) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||
| * | ? | NC_002947 | = 1296609 | 8 (0.110) | 10 (0.220) +48 bp |
9/178 | 4.9 | 33.2% | intergenic (‑362/‑204) | nhaA‑I/PP_1133 | Na(+)/H(+) antiporter NhaA/transposase |
| ? | NC_002947 | 5545626 = | 54 (0.770) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||
| * | ? | NC_002947 | = 4808179 | 0 (0.000) | 15 (0.250) | 11/234 | 5.8 | 37.0% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5988949 | 51 (0.850) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | 5477090 = | 77 (1.100) | 10 (0.200) | 7/192 | 6.2 | 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 = | 40 (0.810) | intergenic (+102/+10) | PP_4813/PP_4814 | PAP2 family protein/DedA family protein/ATP‑dependent protease La domain‑containing protein | |||||
| * | ? | NC_002947 | = 2086450 | NA (NA) | 17 (0.250) | 12/262 | 6.2 | NA | coding (565/1302 nt) | PP_1865 | transposase |
| ? | NC_002947 | = 2086464 | NA (NA) | coding (579/1302 nt) | PP_1865 | transposase | |||||