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 | 699,722 | 0 | A | G | 54.4% | 1.9 / 95.3 | 80 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 1,327,121 | 0 | C | T | 50.9% | 35.5 / 153.8 | 111 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 4,348,705 | 0 | A | G | 44.3% | 59.5 / 122.1 | 97 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 195,634 | 0 | C | T | 37.4% | 117.0 / 134.9 | 139 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 196,879 | 0 | G | A | 31.8% | 29.1 / 13.5 | 22 | V795V (GTG→GTA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 196,390 | 0 | T | C | 30.0% | 96.2 / 50.8 | 70 | D632D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 524,167 | 0 | A | G | 28.6% | 75.6 / 17.0 | 54 | intergenic (+34/‑782) | tyrS/PP_16SC | tyrosine‑‑tRNA ligase/16S ribosomal RNA |
| * | NC_002947 | 441,326 | 0 | G | . | 27.0% | 88.7 / 33.3 | 37 | coding (207/1173 nt) | bioF | 8‑amino‑7‑oxononanoate synthase |
| * | NC_002947 | 4,340,089 | 0 | G | C | 26.3% | 57.8 / 20.3 | 39 | intergenic (+74/‑257) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 196,351 | 0 | C | G | 25.8% | 167.3 / 67.2 | 95 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 4,340,081 | 0 | A | G | 25.8% | 45.6 / 15.1 | 31 | intergenic (+66/‑265) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 195,559 | 0 | C | A | 25.0% | 153.3 / 46.5 | 76 | T355T (ACC→ACA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 5,988,911 | 0 | A | . | 24.8% | 304.8 / 104.7 | 118 | intergenic (+205/‑341) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 2,282,770 | 0 | T | G | 24.6% | 86.6 / 41.0 | 65 | intergenic (‑162/+67) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 5,988,905 | 0 | T | C | 24.2% | 213.8 / 71.2 | 120 | intergenic (+199/‑347) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 4,340,083 | 0 | A | G | 24.1% | 45.0 / 13.1 | 31 | intergenic (+68/‑263) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 5,997,194 | 0 | C | . | 24.1% | 131.6 / 46.5 | 61 | intergenic (‑163/+37) | PP_5252/PP_5253 | hypothetical protein/arylesterase |
| * | NC_002947 | 4,340,082 | 0 | C | T | 23.3% | 50.9 / 12.1 | 31 | intergenic (+67/‑264) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,340,075 | 0 | A | T | 22.9% | 59.2 / 14.6 | 37 | intergenic (+60/‑271) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,340,084 | 0 | C | T | 22.6% | 57.0 / 12.0 | 31 | intergenic (+69/‑262) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| Marginal new junction evidence (lowest skew 10 of 254 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | = 652782 | 47 (0.630) | 20 (0.310) | 19/238 | 3.9 | 49.9% | 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 | = 4808179 | 0 (0.000) | 29 (0.430) | 16/254 | 5.1 | 45.7% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 5988765 = | 69 (1.010) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 5453138 | 4 (0.050) | 14 (0.290) +48 bp |
8/182 | 5.8 | 44.8% | intergenic (+151/‑204) | lnt/PP_4791 | apolipoprotein N‑acyltransferase/transposase |
| ? | NC_002947 | 5545626 = | 49 (0.660) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||
| * | ? | NC_002947 | 5224500 = | 2 (0.030) | 14 (0.290) +48 bp |
8/182 | 5.8 | 45.7% | intergenic (‑204/+175) | PP_4603/PP_4604 | transposase/DMT superfamily permease |
| ? | NC_002947 | 5545626 = | 49 (0.660) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||
| * | ? | NC_002947 | = 4586029 | 16 (0.210) | 16 (0.230) | 14/256 | 5.8 | 35.7% | intergenic (+112/+103) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947 | = 4586109 | 43 (0.630) | intergenic (+192/+23) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947 | 4075618 = | 1 (0.010) | 14 (0.290) +48 bp |
8/182 | 5.8 | 46.2% | intergenic (‑204/+237) | PP_3586/tpx | transposase/2‑Cys peroxiredoxin |
| ? | NC_002947 | 5545626 = | 49 (0.660) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||
| * | ? | NC_002947 | 3828180 = | 3 (0.040) | 14 (0.290) +48 bp |
8/182 | 5.8 | 45.2% | intergenic (‑204/+155) | PP_3381/PP_3382 | transposase/gluconate 2‑dehydrogenase cytochrome c subunit |
| ? | NC_002947 | 5545626 = | 49 (0.660) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||
| * | ? | NC_002947 | 2939258 = | 7 (0.090) | 14 (0.290) +48 bp |
8/182 | 5.8 | 43.4% | intergenic (‑204/+236) | PP_2570/PP_2572 | transposase/hypothetical protein |
| ? | NC_002947 | 5545626 = | 49 (0.660) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||
| * | ? | NC_002947 | = 1440124 | 5 (0.070) | 14 (0.290) +48 bp |
8/182 | 5.8 | 44.3% | intergenic (‑455/‑204) | yveA/PP_1260 | aspartate‑proton symporter/transposase |
| ? | NC_002947 | 5545626 = | 49 (0.660) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||
| * | ? | NC_002947 | = 1296609 | 6 (0.080) | 14 (0.290) +48 bp |
8/182 | 5.8 | 43.8% | intergenic (‑362/‑204) | nhaA‑I/PP_1133 | Na(+)/H(+) antiporter NhaA/transposase |
| ? | NC_002947 | 5545626 = | 49 (0.660) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||