mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 225 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 1,327,127 | 0 | C | T | 50.8% | 192.5 / inf | 528 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 4,350,671 | 0 | A | G | 50.3% | 167.2 / inf | 555 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 4,810,147 | 0 | A | C | 50.0% | ‑2.9 / 151.2 | 100 | intergenic (‑289/‑266) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 4,810,148 | 0 | A | G | 50.0% | ‑4.6 / 141.7 | 100 | intergenic (‑290/‑265) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 699,725 | 0 | A | G | 47.8% | 106.3 / inf | 387 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 1,544,531 | 0 | C | A | 45.1% | 137.7 / inf | 257 | intergenic (+48/+66) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,544,543 | 0 | G | C | 44.9% | 149.6 / inf | 248 | intergenic (+60/+54) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,544,534 | 0 | G | C | 44.5% | 157.2 / inf | 263 | intergenic (+51/+63) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 2,284,735 | 0 | T | G | 44.2% | 172.5 / inf | 355 | intergenic (‑162/+67) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 1,544,536 | 0 | C | G | 43.7% | 172.1 / inf | 248 | intergenic (+53/+61) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,544,546 | 0 | T | G | 43.6% | 130.3 / inf | 252 | intergenic (+63/+51) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 4,342,049 | 0 | A | G | 43.6% | 104.3 / 182.8 | 150 | intergenic (+68/‑263) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,342,048 | 0 | C | T | 43.3% | 105.1 / 183.4 | 150 | intergenic (+67/‑264) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,342,050 | 0 | C | T | 43.3% | 102.1 / 185.1 | 150 | intergenic (+69/‑262) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 2,284,744 | 0 | C | A | 42.9% | 239.8 / inf | 353 | intergenic (‑171/+58) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 4,342,047 | 0 | A | G | 42.8% | 115.3 / 182.1 | 152 | intergenic (+66/‑265) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 1,544,541 | 0 | C | G | 42.7% | 185.3 / inf | 248 | intergenic (+58/+56) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 5,742,449 | 0 | A | T | 42.3% | 66.6 / 218.4 | 188 | intergenic (+36/+35) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947 | 5,742,445 | 0 | T | G | 42.0% | 84.6 / 240.5 | 189 | intergenic (+32/+39) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947 | 2,284,740 | 0 | G | C | 40.9% | 287.0 / inf | 336 | intergenic (‑167/+62) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| Marginal new junction evidence (lowest skew 10 of 346 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | 4810141 = | 71 (0.200) | 211 (0.810) | 78/208 | 3.0 | 59.9% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5990913 | 230 (0.890) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 652785 | 326 (0.940) | 150 (0.510) | 73/238 | 5.2 | 51.8% | coding (1961/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947 | = 4810126 | 0 (0.000) | intergenic (‑268/‑287) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947 | = 4810146 | 50 (0.140) | 163 (0.510) | 75/254 | 5.8 | 45.7% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 5990743 = | 342 (1.080) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | 4898345 = | 239 (0.690) | 104 (0.350) | 53/236 | 8.8 | 32.3% | intergenic (+11/‑197) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein |
| ? | NC_002947 | 4898434 = | 233 (0.790) | intergenic (+100/‑108) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein | |||||
| * | ? | NC_002947 | = 4810146 | 50 (0.140) | 104 (0.350) | 50/238 | 9.6 | 37.4% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5990927 | 306 (1.030) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 5455108 | 23 (0.070) | 42 (0.180) +48 bp |
27/182 | 12.4 | 34.9% | intergenic (+151/‑204) | lnt/PP_4791 | apolipoprotein N‑acyltransferase/transposase |
| ? | NC_002947 | 5547596 = | 216 (0.620) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||
| * | ? | NC_002947 | 5226470 = | 27 (0.080) | 42 (0.180) +48 bp |
27/182 | 12.4 | 34.6% | intergenic (‑204/+175) | PP_4603/PP_4604 | transposase/DMT superfamily permease |
| ? | NC_002947 | 5547596 = | 216 (0.620) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||
| * | ? | NC_002947 | 4077584 = | 12 (0.030) | 42 (0.180) +48 bp |
27/182 | 12.4 | 36.0% | intergenic (‑204/+237) | PP_3586/tpx | transposase/2‑Cys peroxiredoxin |
| ? | NC_002947 | 5547596 = | 216 (0.620) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||
| * | ? | NC_002947 | 3830145 = | 20 (0.060) | 42 (0.180) +48 bp |
27/182 | 12.4 | 35.2% | intergenic (‑204/+155) | PP_3381/PP_3382 | transposase/gluconate 2‑dehydrogenase cytochrome c subunit |
| ? | NC_002947 | 5547596 = | 216 (0.620) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||
| * | ? | NC_002947 | 2941223 = | 23 (0.070) | 42 (0.180) +48 bp |
27/182 | 12.4 | 34.9% | intergenic (‑204/+236) | PP_2570/PP_2572 | transposase/hypothetical protein |
| ? | NC_002947 | 5547596 = | 216 (0.620) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||