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 38 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 | 55.8% | 3.3 / 102.0 | 87 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 4,348,705 | 0 | A | G | 48.2% | 41.5 / 159.1 | 114 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 699,722 | 0 | A | G | 47.8% | 11.0 / 91.8 | 69 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 195,634 | 0 | C | T | 38.3% | 96.7 / 110.8 | 109 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 5,988,905 | 0 | T | C | 36.1% | 67.4 / 67.6 | 72 | intergenic (+199/‑347) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,988,911 | 0 | A | . | 35.1% | 164.2 / 98.7 | 74 | intergenic (+205/‑341) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 1,544,501 | 0 | G | C | 34.8% | 21.3 / 18.9 | 24 | intergenic (+60/+54) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,544,494 | 0 | C | G | 33.3% | 23.5 / 18.7 | 24 | intergenic (+53/+61) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,544,499 | 0 | C | G | 33.3% | 17.5 / 17.9 | 24 | intergenic (+58/+56) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,544,489 | 0 | C | A | 32.0% | 22.0 / 18.9 | 25 | intergenic (+48/+66) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,544,492 | 0 | G | C | 32.0% | 30.9 / 19.0 | 25 | intergenic (+51/+63) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,544,504 | 0 | T | G | 32.0% | 30.3 / 17.4 | 25 | intergenic (+63/+51) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 196,351 | 0 | C | G | 31.6% | 132.0 / 85.7 | 96 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 1,126,602 | 0 | C | A | 31.4% | 57.4 / 11.1 | 35 | intergenic (‑56/+93) | tdcG‑II/gcvP‑I | L‑serine dehydratase/glycine dehydrogenase |
| * | NC_002947 | 5,988,894 | 0 | C | T | 29.0% | 104.8 / 48.0 | 69 | intergenic (+188/‑358) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,988,895 | 0 | A | G | 29.0% | 100.3 / 49.7 | 69 | intergenic (+189/‑357) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 195,559 | 0 | C | A | 28.9% | 139.3 / 58.1 | 77 | T355T (ACC→ACA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 196,327 | 0 | A | C | 27.8% | 153.9 / 79.0 | 98 | T611T (ACA→ACC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 5,988,889 | 0 | C | A | 27.7% | 121.9 / 41.0 | 65 | intergenic (+183/‑363) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,740,467 | 0 | T | G | 26.8% | 39.0 / 24.5 | 41 | intergenic (+32/+39) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| Marginal new junction evidence (lowest skew 10 of 388 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | = 4586029 | 6 (0.110) | 19 (0.370) | 15/254 | 3.4 | 62.8% | intergenic (+112/+103) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947 | = 4586109 | 17 (0.330) | intergenic (+192/+23) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947 | = 652782 | 44 (0.790) | 10 (0.210) | 9/236 | 4.9 | 34.7% | 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 | = 1436099 | 64 (1.150) | 15 (0.300) | 9/252 | 5.2 | 26.2% | intergenic (‑136/+17) | PP_1256/PP_1257 | alpha‑ketoglutarate semialdehyde dehydrogenase/1‑pyrroline‑4‑hydroxy‑2‑carboxylate deaminase |
| ? | NC_002947 | 1499519 = | 26 (0.510) | intergenic (+96/‑68) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein | |||||
| * | ? | NC_002947 | = 5786495 | 77 (1.390) | 8 (0.170) | 7/228 | 5.5 | 12.9% | intergenic (+38/‑93) | PP_5068/trxC | hypothetical protein/thioredoxin |
| ? | NC_002947 | = 5786532 | 44 (0.960) | intergenic (+75/‑56) | PP_5068/trxC | hypothetical protein/thioredoxin | |||||
| * | ? | NC_002947 | 5914157 = | 44 (0.790) | 6 (0.140) | 6/220 | 5.7 | 16.4% | intergenic (+49/+104) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase |
| ? | NC_002947 | 5914253 = | 26 (0.590) | intergenic (+145/+8) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase | |||||
| * | ? | NC_002947 | 1731163 = | 47 (0.850) | 6 (0.140) | 6/220 | 5.7 | 13.4% | intergenic (‑76/+115) | dapE/PP_1526 | succinyl‑diaminopimelate desuccinylase/beta‑(1‑3)‑glucosyl transferase |
| ? | NC_002947 | 1731255 = | 40 (0.900) | intergenic (‑168/+23) | dapE/PP_1526 | succinyl‑diaminopimelate desuccinylase/beta‑(1‑3)‑glucosyl transferase | |||||
| * | ? | NC_002947 | = 2236934 | 74 (1.330) | 7 (0.140) | 7/244 | 5.8 | 10.0% | intergenic (+29/+99) | uvrB/PP_1975 | uvrABC excinuclease protein B/EmrB/QacA family drug resistance transporter |
| ? | NC_002947 | = 2236993 | 60 (1.220) | intergenic (+88/+40) | uvrB/PP_1975 | uvrABC excinuclease protein B/EmrB/QacA family drug resistance transporter | |||||
| * | ? | NC_002947 | = 1114894 | 46 (0.830) | 8 (0.180) | 6/226 | 5.9 | 17.8% | intergenic (‑88/+91) | rlmF/valS | ribosomal RNA large subunit methyltransferase F/valine‑‑tRNA ligase |
| ? | NC_002947 | = 1114920 | 36 (0.790) | intergenic (‑114/+65) | rlmF/valS | ribosomal RNA large subunit methyltransferase F/valine‑‑tRNA ligase | |||||
| * | ? | NC_002947 | = 5594119 | 44 (0.790) | 5 (0.110) | 5/220 | 6.2 | 11.6% | intergenic (‑66/+79) | PP_4921/thiC | NCS1 family transporter/phosphomethylpyrimidine synthase |
| ? | NC_002947 | = 5594156 | 41 (0.930) | intergenic (‑103/+42) | PP_4921/thiC | NCS1 family transporter/phosphomethylpyrimidine synthase | |||||
| * | ? | NC_002947 | = 1168581 | 57 (1.030) | 6 (0.120) | 6/240 | 6.2 | 10.8% | intergenic (+98/+155) | eda/leuA | KHG/KDPG aldolase/2‑isopropylmalate synthase |
| ? | NC_002947 | = 1168654 | 50 (1.040) | intergenic (+171/+82) | eda/leuA | KHG/KDPG aldolase/2‑isopropylmalate synthase | |||||