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 43 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 | 52.9% | 3.8 / 86.7 | 70 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 1,327,121 | 0 | C | T | 48.8% | 42.4 / 172.0 | 125 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 4,348,705 | 0 | A | G | 47.7% | 27.5 / 118.3 | 88 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 195,634 | 0 | C | T | 43.2% | 57.7 / 129.3 | 111 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 5,988,905 | 0 | T | C | 30.4% | 86.5 / 50.1 | 70 | intergenic (+199/‑347) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,988,911 | 0 | A | . | 29.4% | 162.1 / 70.7 | 69 | intergenic (+205/‑341) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 1,703,250 | 0 | G | C | 28.8% | 92.8 / 43.9 | 66 | intergenic (+99/‑68) | lysS/PP_1497 | lysine‑‑tRNA ligase/TetR family transcriptional regulator |
| * | NC_002947 | 195,559 | 0 | C | A | 26.3% | 139.3 / 45.2 | 76 | T355T (ACC→ACA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 753,568 | 0 | G | T | 26.3% | 106.5 / 34.8 | 57 | intergenic (‑807/‑176) | PP_0641/PP_5452 | hypothetical protein/hypothetical protein |
| * | NC_002947 | 1,703,248 | 0 | A | G | 26.2% | 97.7 / 35.4 | 65 | intergenic (+97/‑70) | lysS/PP_1497 | lysine‑‑tRNA ligase/TetR family transcriptional regulator |
| * | NC_002947 | 1,544,489 | 0 | C | A | 25.5% | 90.2 / 28.8 | 47 | intergenic (+48/+66) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,544,492 | 0 | G | C | 25.0% | 89.8 / 28.5 | 48 | intergenic (+51/+63) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,703,252 | 0 | C | T | 25.0% | 102.3 / 34.8 | 66 | intergenic (+101/‑66) | lysS/PP_1497 | lysine‑‑tRNA ligase/TetR family transcriptional regulator |
| * | NC_002947 | 5,903,165 | 0 | A | C | 25.0% | 70.5 / 20.0 | 46 | intergenic (‑129/‑139) | PP_5175/PP_5176 | HlyD family secretion protein/hypothetical protein |
| * | NC_002947 | 1,544,494 | 0 | C | G | 24.5% | 100.3 / 29.6 | 49 | intergenic (+53/+61) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,544,499 | 0 | C | G | 24.5% | 93.9 / 28.3 | 49 | intergenic (+58/+56) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,544,501 | 0 | G | C | 24.5% | 88.7 / 26.3 | 49 | intergenic (+60/+54) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 3,578,433 | 0 | G | T | 24.2% | 122.9 / 14.1 | 66 | intergenic (+110/‑214) | PP_3158/PP_5589 | hypothetical protein/rhs repeat‑associated core domain‑containing protein |
| * | NC_002947 | 5,988,895 | 0 | A | G | 24.2% | 115.5 / 35.6 | 66 | intergenic (+189/‑357) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 697,228 | 0 | C | G | 23.6% | 176.8 / 52.4 | 89 | intergenic (+155/‑596) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| Marginal new junction evidence (lowest skew 10 of 611 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | = 4808179 | 0 (0.000) | 17 (0.280) | 14/260 | 4.7 | 34.7% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 5988765 = | 64 (1.050) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 5453138 | 5 (0.080) | 7 (0.160) +48 bp |
7/188 | 5.3 | 28.2% | intergenic (+151/‑204) | lnt/PP_4791 | apolipoprotein N‑acyltransferase/transposase |
| ? | NC_002947 | 5545626 = | 49 (0.740) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||
| * | ? | NC_002947 | 5224500 = | 5 (0.080) | 7 (0.160) +48 bp |
7/188 | 5.3 | 28.2% | intergenic (‑204/+175) | PP_4603/PP_4604 | transposase/DMT superfamily permease |
| ? | NC_002947 | 5545626 = | 49 (0.740) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||
| * | ? | NC_002947 | 4075618 = | 11 (0.170) | 7 (0.160) +48 bp |
7/188 | 5.3 | 26.1% | intergenic (‑204/+237) | PP_3586/tpx | transposase/2‑Cys peroxiredoxin |
| ? | NC_002947 | 5545626 = | 49 (0.740) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||
| * | ? | NC_002947 | 3828180 = | 6 (0.090) | 7 (0.160) +48 bp |
7/188 | 5.3 | 27.9% | intergenic (‑204/+155) | PP_3381/PP_3382 | transposase/gluconate 2‑dehydrogenase cytochrome c subunit |
| ? | NC_002947 | 5545626 = | 49 (0.740) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||
| * | ? | NC_002947 | 2939258 = | 6 (0.090) | 7 (0.160) +48 bp |
7/188 | 5.3 | 27.9% | intergenic (‑204/+236) | PP_2570/PP_2572 | transposase/hypothetical protein |
| ? | NC_002947 | 5545626 = | 49 (0.740) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||
| * | ? | NC_002947 | = 1440124 | 8 (0.120) | 7 (0.160) +48 bp |
7/188 | 5.3 | 27.1% | intergenic (‑455/‑204) | yveA/PP_1260 | aspartate‑proton symporter/transposase |
| ? | NC_002947 | 5545626 = | 49 (0.740) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||
| * | ? | NC_002947 | = 1296609 | 7 (0.110) | 7 (0.160) +48 bp |
7/188 | 5.3 | 27.5% | intergenic (‑362/‑204) | nhaA‑I/PP_1133 | Na(+)/H(+) antiporter NhaA/transposase |
| ? | NC_002947 | 5545626 = | 49 (0.740) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||
| * | ? | NC_002947 | = 1419549 | 37 (0.560) | 14 (0.220) | 13/278 | 5.4 | 25.9% | intergenic (‑38/+98) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein |
| ? | NC_002947 | = 1419636 | 44 (0.680) | intergenic (‑125/+11) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein | |||||
| * | ? | NC_002947 | 1906682 = | 43 (0.650) | 10 (0.180) | 9/232 | 5.7 | 22.0% | intergenic (+22/+106) | nirD/PP_1707 | nitrite reductase/D‑isomer specific 2‑hydroxyacid dehydrogenase family protein |
| ? | NC_002947 | 1906776 = | 36 (0.660) | intergenic (+116/+12) | nirD/PP_1707 | nitrite reductase/D‑isomer specific 2‑hydroxyacid dehydrogenase family protein | |||||