mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.2 revision caddc01d3be9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 76 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 4,741,273 | 1 | . | C | 69.0% | 65.6 / 27.6 | 29 | intergenic (+464/+288) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,275 | 0 | A | G | 69.0% | 35.4 / 17.1 | 29 | intergenic (+466/+286) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,298 | 1 | . | T | 66.7% | 74.8 / 37.5 | 33 | intergenic (+489/+263) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,302 | 0 | A | G | 66.7% | 34.7 / 23.3 | 33 | intergenic (+493/+259) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,305 | 0 | A | . | 66.7% | 43.1 / 44.0 | 33 | intergenic (+496/+256) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 699,725 | 0 | A | G | 56.9% | 4.0 / 57.8 | 52 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 1,327,127 | 0 | C | T | 56.4% | ‑1.1 / 113.9 | 94 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 4,842,941 | 0 | C | . | 51.8% | 87.0 / 129.5 | 56 | intergenic (+40/‑257) | ccoP‑II/PP_4259 | cbb3‑type cytochrome c oxidase subunit/iron‑sulfur cluster‑binding protein |
| * | NC_002947 | 4,348,749 | 0 | A | G | 48.5% | 24.4 / 136.5 | 101 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 4,842,949 | 1 | . | G | 47.2% | 13.7 / 116.6 | 53 | intergenic (+48/‑249) | ccoP‑II/PP_4259 | cbb3‑type cytochrome c oxidase subunit/iron‑sulfur cluster‑binding protein |
| * | NC_002947 | 2,282,813 | 0 | T | G | 42.9% | 31.6 / 69.1 | 56 | intergenic (‑162/+67) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 5,655,682 | 0 | T | G | 41.0% | 43.1 / 98.6 | 78 | intergenic (‑86/+66) | epd/tktA | D‑erythrose 4‑phosphate dehydrogenase/transketolase A |
| * | NC_002947 | 2,282,822 | 0 | C | A | 40.7% | 55.4 / 56.5 | 54 | intergenic (‑171/+58) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 5,655,687 | 0 | C | A | 39.5% | 75.8 / 82.7 | 76 | intergenic (‑91/+61) | epd/tktA | D‑erythrose 4‑phosphate dehydrogenase/transketolase A |
| * | NC_002947 | 2,282,817 | 0 | G | C | 37.9% | 71.0 / 66.3 | 58 | intergenic (‑166/+63) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 2,282,818 | 0 | G | C | 37.9% | 64.7 / 67.5 | 58 | intergenic (‑167/+62) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 195,634 | 0 | C | T | 35.7% | 137.0 / 119.8 | 130 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 4,951,017 | 0 | T | G | 34.0% | 46.4 / 43.5 | 53 | intergenic (‑122/+35) | fliL/fliK | flagellar protein FliL/flagellar hook‑length control protein FliK |
| * | NC_002947 | 4,049,954 | 0 | C | G | 33.3% | 69.3 / 52.9 | 58 | intergenic (+43/‑58) | quiA/oprB‑III | quinate dehydrogenase/carbohydrate‑selective porin |
| * | NC_002947 | 4,741,299 | 0 | C | T | 33.3% | 35.9 / 22.9 | 33 | intergenic (+490/+262) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| Marginal new junction evidence (lowest skew 10 of 1152 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | 4896423 = | 59 (0.770) | 24 (0.370) | 20/224 | 3.1 | 34.6% | intergenic (+11/‑197) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein |
| ? | NC_002947 | 4896512 = | 41 (0.640) | intergenic (+100/‑108) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein | |||||
| * | ? | NC_002947 | = 5201663 | 62 (0.810) | 18 (0.330) | 16/192 | 3.2 | 30.3% | intergenic (‑101/‑79) | PP_4582/PP_4583 | membrane protein/putative Peptidase |
| ? | NC_002947 | = 5201684 | 38 (0.690) | intergenic (‑122/‑58) | PP_4582/PP_4583 | membrane protein/putative Peptidase | |||||
| * | ? | NC_002947 | 1967188 = | 37 (0.480) | 25 (0.440) | 17/200 | 3.2 | 46.4% | intergenic (+15/+104) | PP_1762/yciK | hypothetical protein/putative oxidoreductase |
| ? | NC_002947 | 1967284 = | 30 (0.520) | intergenic (+111/+8) | PP_1762/yciK | hypothetical protein/putative oxidoreductase | |||||
| * | ? | NC_002947 | = 176399 | NA (NA) | 57 (0.770) +CGAAA |
23/256 | 3.2 | 34.0% | intergenic (+43/‑420) | PP_5SA/PP_16SB | 5S ribosomal RNA/16S ribosomal RNA |
| ? | NC_002947 | = 182013 | 115 (1.500) | intergenic (+2/+63) | PP_5SB/PP_0160 | 5S ribosomal RNA/ferrioxamine receptor | |||||
| * | ? | NC_002947 | = 5506637 | 68 (0.890) | 27 (0.450) | 17/208 | 3.3 | 36.7% | intergenic (+48/‑151) | PP_4839/cycA | iron‑regulated membrane protein/D‑alanine/beta‑alanine/D‑serine/glycine permease |
| ? | NC_002947 | = 5506650 | 40 (0.670) | intergenic (+61/‑138) | PP_4839/cycA | iron‑regulated membrane protein/D‑alanine/beta‑alanine/D‑serine/glycine permease | |||||
| * | ? | NC_002947 | = 4586100 | 54 (0.710) | 17 (0.310) | 14/190 | 3.6 | 38.9% | intergenic (+139/+78) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947 | = 4586128 | 15 (0.280) | intergenic (+167/+50) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947 | = 6006630 | 33 (0.430) | 20 (0.360) | 14/194 | 3.7 | 47.6% | intergenic (+42/+57) | ydcJ/PP_5261 | metalloprotein/LysR family transcriptional regulator |
| ? | NC_002947 | = 6006642 | 20 (0.360) | intergenic (+54/+45) | ydcJ/PP_5261 | metalloprotein/LysR family transcriptional regulator | |||||
| * | ? | NC_002947 | 5477138 = | 74 (0.970) | 24 (0.450) | 13/184 | 3.7 | 42.5% | intergenic (+3/+109) | PP_4813/PP_4814 | PAP2 family protein/DedA family protein/ATP‑dependent protease La domain‑containing protein |
| ? | NC_002947 | 5477237 = | 14 (0.270) | intergenic (+102/+10) | PP_4813/PP_4814 | PAP2 family protein/DedA family protein/ATP‑dependent protease La domain‑containing protein | |||||
| * | ? | NC_002947 | = 202378 | 74 (0.970) | 20 (0.380) +41 bp |
13/184 | 3.7 | 28.3% | coding (7884/26049 nt) | PP_0168 | putative surface adhesion protein |
| ? | NC_002947 | = 217036 | 73 (0.950) | coding (22542/26049 nt) | PP_0168 | putative surface adhesion protein | |||||
| * | ? | NC_002947 | = 202378 | 74 (0.970) | 20 (0.380) +41 bp |
13/184 | 3.7 | 27.9% | coding (7884/26049 nt) | PP_0168 | putative surface adhesion protein |
| ? | NC_002947 | = 213736 | 76 (0.990) | coding (19242/26049 nt) | PP_0168 | putative surface adhesion protein | |||||