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 64 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 4,741,298 | 1 | . | T | 72.0% | 123.1 / 45.3 | 50 | intergenic (+489/+263) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,302 | 0 | A | G | 72.0% | 78.3 / 24.8 | 50 | intergenic (+493/+259) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,305 | 0 | A | . | 72.0% | 91.8 / 58.6 | 50 | intergenic (+496/+256) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,273 | 1 | . | C | 66.7% | 92.6 / 47.3 | 42 | intergenic (+464/+288) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,275 | 0 | A | G | 66.7% | 45.5 / 30.4 | 42 | intergenic (+466/+286) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 1,327,127 | 0 | C | T | 49.1% | 48.7 / 166.8 | 118 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 4,348,749 | 0 | A | G | 43.9% | 55.4 / 140.1 | 123 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 195,634 | 0 | C | T | 40.2% | 148.5 / 221.3 | 205 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 699,725 | 0 | A | G | 37.8% | 98.3 / 113.5 | 119 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 4,741,274 | 0 | A | C | 33.3% | 51.6 / 27.5 | 42 | intergenic (+465/+287) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,842,949 | 1 | . | G | 31.9% | 173.7 / 161.1 | 113 | intergenic (+48/‑249) | ccoP‑II/PP_4259 | cbb3‑type cytochrome c oxidase subunit/iron‑sulfur cluster‑binding protein |
| * | NC_002947 | 2,951,377 | 0 | G | C | 30.2% | 124.6 / 79.1 | 88 | intergenic (‑113/+48) | oguA/PP_2585 | 8‑oxoguanine deaminase/alpha‑ketoglutaric semialdehyde dehydrogenase |
| * | NC_002947 | 4,842,941 | 0 | C | . | 29.8% | 267.6 / 125.4 | 114 | intergenic (+40/‑257) | ccoP‑II/PP_4259 | cbb3‑type cytochrome c oxidase subunit/iron‑sulfur cluster‑binding protein |
| * | NC_002947 | 2,951,385 | 0 | G | T | 29.5% | 127.3 / 63.8 | 88 | intergenic (‑121/+40) | oguA/PP_2585 | 8‑oxoguanine deaminase/alpha‑ketoglutaric semialdehyde dehydrogenase |
| * | NC_002947 | 2,951,392 | 0 | G | C | 29.4% | 139.6 / 69.1 | 85 | intergenic (‑128/+33) | oguA/PP_2585 | 8‑oxoguanine deaminase/alpha‑ketoglutaric semialdehyde dehydrogenase |
| * | NC_002947 | 2,951,384 | 0 | A | C | 28.4% | 113.8 / 68.4 | 88 | intergenic (‑120/+41) | oguA/PP_2585 | 8‑oxoguanine deaminase/alpha‑ketoglutaric semialdehyde dehydrogenase |
| * | NC_002947 | 4,741,299 | 0 | C | T | 28.0% | 76.8 / 26.4 | 50 | intergenic (+490/+262) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,301 | 0 | A | C | 28.0% | 71.1 / 33.3 | 50 | intergenic (+492/+260) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,304 | 0 | C | G | 28.0% | 92.8 / 32.7 | 50 | intergenic (+495/+257) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 196,390 | 0 | T | C | 27.3% | 173.5 / 64.6 | 99 | D632D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| Marginal new junction evidence (lowest skew 10 of 1111 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | 4808219 = | 7 (0.080) | 30 (0.440) | 21/206 | 3.2 | 42.5% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5988991 | 76 (1.130) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 2553944 | NA (NA) | 70 (0.840) | 27/254 | 3.2 | 51.0% | intergenic (+32/‑119) | PP_5SF/PP_2240 | 5S ribosomal RNA/ABC transporter permease/ATP‑binding protein |
| ? | NC_002947 | 5307467 = | 73 (0.810) | intergenic (‑168/+18) | recC/PP_5SG | multifunctional ATP‑dependent DNA helicase/dsDNA/ssDNA exonuclease/ssDNA endonuclease recombinase subunit/5S ribosomal RNA | |||||
| * | ? | NC_002947 | = 652785 | 71 (0.780) | 31 (0.400) | 25/236 | 3.2 | 50.6% | coding (1961/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947 | = 4808204 | 0 (0.000) | intergenic (‑268/‑287) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947 | 1544501 = | 90 (0.990) | 32 (0.450) | 22/216 | 3.3 | 33.1% | intergenic (+18/+96) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| ? | NC_002947 | 1544577 = | 59 (0.830) | intergenic (+94/+20) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG | |||||
| * | ? | NC_002947 | 413997 = | 112 (1.240) | 23 (0.320) | 20/220 | 3.8 | 20.8% | intergenic (+14/‑189) | glnE/waaF | glutamate‑ammonia‑ligase adenylyltransferase/ADP‑heptose:LPS heptosyltransferase II |
| ? | NC_002947 | 414083 = | 86 (1.190) | intergenic (+100/‑103) | glnE/waaF | glutamate‑ammonia‑ligase adenylyltransferase/ADP‑heptose:LPS heptosyltransferase II | |||||
| * | ? | NC_002947 | = 4808224 | 15 (0.170) | 37 (0.450) | 21/252 | 4.3 | 38.2% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 5988821 = | 106 (1.280) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 4808224 | 15 (0.170) | 30 (0.390) | 18/236 | 4.6 | 37.1% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5989005 | 89 (1.150) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 1114899 | 105 (1.160) | 17 (0.230) | 17/226 | 4.6 | 16.8% | intergenic (‑88/+91) | rlmF/valS | ribosomal RNA large subunit methyltransferase F/valine‑‑tRNA ligase |
| ? | NC_002947 | = 1114925 | 83 (1.120) | intergenic (‑114/+65) | rlmF/valS | ribosomal RNA large subunit methyltransferase F/valine‑‑tRNA ligase | |||||
| * | ? | NC_002947 | 1967188 = | 60 (0.660) | 21 (0.310) | 14/210 | 5.0 | 31.4% | intergenic (+15/+104) | PP_1762/yciK | hypothetical protein/putative oxidoreductase |
| ? | NC_002947 | 1967284 = | 46 (0.670) | intergenic (+111/+8) | PP_1762/yciK | hypothetical protein/putative oxidoreductase | |||||
| * | ? | NC_002947 | = 4586100 | 77 (0.850) | 15 (0.230) | 13/200 | 5.1 | 21.5% | intergenic (+139/+78) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947 | = 4586128 | 54 (0.820) | intergenic (+167/+50) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||