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 36 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 1,327,121 | 0 | C | T | 53.5% | 17.5 / 125.4 | 100 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 699,722 | 0 | A | G | 46.8% | 23.6 / 102.8 | 79 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 4,348,705 | 0 | A | G | 46.2% | 65.5 / 175.5 | 132 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 195,634 | 0 | C | T | 41.3% | 87.5 / 138.5 | 123 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 5,988,905 | 0 | T | C | 33.8% | 88.6 / 69.5 | 80 | intergenic (+199/‑347) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,988,911 | 0 | A | . | 32.9% | 194.8 / 105.5 | 85 | intergenic (+205/‑341) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 1,544,501 | 0 | G | C | 32.0% | 31.3 / 18.6 | 26 | intergenic (+60/+54) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 195,559 | 0 | C | A | 30.9% | 143.0 / 67.4 | 86 | T355T (ACC→ACA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 1,544,489 | 0 | C | A | 30.8% | 24.9 / 18.8 | 26 | intergenic (+48/+66) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,544,494 | 0 | C | G | 30.8% | 29.7 / 18.4 | 26 | intergenic (+53/+61) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,544,499 | 0 | C | G | 30.8% | 26.1 / 17.5 | 26 | intergenic (+58/+56) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,126,602 | 0 | C | A | 30.0% | 67.6 / 11.5 | 40 | intergenic (‑56/+93) | tdcG‑II/gcvP‑I | L‑serine dehydratase/glycine dehydrogenase |
| * | NC_002947 | 1,544,492 | 0 | G | C | 29.6% | 34.2 / 18.7 | 27 | intergenic (+51/+63) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,544,504 | 0 | T | G | 29.6% | 40.3 / 17.0 | 27 | intergenic (+63/+51) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 196,351 | 0 | C | G | 29.2% | 163.8 / 87.5 | 108 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 5,988,894 | 0 | C | T | 27.3% | 126.4 / 50.1 | 77 | intergenic (+188/‑358) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,988,895 | 0 | A | G | 27.3% | 121.6 / 51.7 | 77 | intergenic (+189/‑357) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,988,889 | 0 | C | A | 26.4% | 142.9 / 43.8 | 72 | intergenic (+183/‑363) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 1,703,250 | 0 | G | C | 26.2% | 83.8 / 37.5 | 61 | intergenic (+99/‑68) | lysS/PP_1497 | lysine‑‑tRNA ligase/TetR family transcriptional regulator |
| * | NC_002947 | 196,327 | 0 | A | C | 25.9% | 184.9 / 78.7 | 109 | T611T (ACA→ACC) | PP_0168 | putative surface adhesion protein |
| Marginal new junction evidence (lowest skew 10 of 503 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | = 4586029 | 7 (0.110) | 20 (0.350) | 15/254 | 4.1 | 59.3% | intergenic (+112/+103) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947 | = 4586109 | 21 (0.360) | intergenic (+192/+23) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947 | = 4808179 | 0 (0.000) | 24 (0.420) | 13/252 | 4.7 | 46.6% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 5988765 = | 55 (0.960) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 652782 | 52 (0.830) | 12 (0.220) | 11/236 | 4.9 | 35.1% | 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 | = 6060444 | 72 (1.140) | 10 (0.180) | 10/248 | 5.6 | 12.9% | intergenic (+80/+101) | PP_5311/PP_5312 | signal transduction protein/hypothetical protein |
| ? | NC_002947 | = 6060503 | 70 (1.240) | intergenic (+139/+42) | PP_5311/PP_5312 | signal transduction protein/hypothetical protein | |||||
| * | ? | NC_002947 | 1499507 = | 29 (0.460) | 19 (0.330) | 10/252 | 5.7 | 27.6% | intergenic (+84/‑80) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| ? | NC_002947 | = 6060505 | 73 (1.270) | intergenic (+141/+40) | PP_5311/PP_5312 | signal transduction protein/hypothetical protein | |||||
| * | ? | NC_002947 | = 5786495 | 86 (1.370) | 9 (0.170) | 8/228 | 5.9 | 13.0% | intergenic (+38/‑93) | PP_5068/trxC | hypothetical protein/thioredoxin |
| ? | NC_002947 | = 5786532 | 50 (0.960) | intergenic (+75/‑56) | PP_5068/trxC | hypothetical protein/thioredoxin | |||||
| * | ? | NC_002947 | = 1114894 | 51 (0.810) | 9 (0.170) | 7/226 | 6.2 | 18.2% | intergenic (‑88/+91) | rlmF/valS | ribosomal RNA large subunit methyltransferase F/valine‑‑tRNA ligase |
| ? | NC_002947 | = 1114920 | 39 (0.760) | intergenic (‑114/+65) | rlmF/valS | ribosomal RNA large subunit methyltransferase F/valine‑‑tRNA ligase | |||||
| * | ? | NC_002947 | = 2099982 | 36 (0.570) | 8 (0.150) | 7/230 | 6.4 | 18.2% | intergenic (‑93/‑112) | PP_1875/PP_1876 | two‑component system sensor histidine kinase/response regulator/AAA family ATP/GTP‑binding protein |
| ? | NC_002947 | = 2100031 | 42 (0.800) | intergenic (‑142/‑63) | PP_1875/PP_1876 | two‑component system sensor histidine kinase/response regulator/AAA family ATP/GTP‑binding protein | |||||
| * | ? | NC_002947 | = 1311719 | 51 (0.810) | 8 (0.140) | 8/250 | 6.4 | 15.2% | intergenic (‑187/+91) | PP_1144/rapA | membrane protein/RNA polymerase‑associated protein RapA |
| ? | NC_002947 | = 1311778 | 43 (0.750) | intergenic (‑246/+32) | PP_1144/rapA | membrane protein/RNA polymerase‑associated protein RapA | |||||
| * | ? | NC_002947 | = 5453138 | 3 (0.050) | 4 (0.100) +48 bp |
4/180 | 6.5 | 26.5% | intergenic (+151/‑204) | lnt/PP_4791 | apolipoprotein N‑acyltransferase/transposase |
| ? | NC_002947 | 5545626 = | 31 (0.490) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||