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espinos:results.coverage.analysis [2015/08/06 19:06] cespinos |
espinos:results.coverage.analysis [2015/08/12 11:05] (current) cespinos [2.2 Coverage Analysis - All exome coverage] |
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| ====== 2.2 Coverage Analysis - All exome coverage ====== | ====== 2.2 Coverage Analysis - All exome coverage ====== | ||
| - | ===== BIER's pipeline ===== | + | Here, we show an overview of all exome coverage obtained after processing reads in each pipeline. Main statistical indicators included in each table: |
| - | ^ Sample ^ Total_cov_bases ^ Mean_Cov ^ Median_Cov ^ %_bases_>15 ^ %_bases_>30 ^ %_bases_>40 ^ %_bases_>50 ^ | + | * **Total_Cov_bases**: total sum of all base pairs coverage of each interval (exome capture kit target) |
| + | * **Mean_Cov, Median_Cov**: mean and median coverage of all intervals | ||
| + | * **%_bases_>15, >30, >40, >50**: percentage of intervals base pairs covered by more than 15, 30, 40 or 50 reads | ||
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| + | ==== BIER's pipeline ==== | ||
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| + | ^ Sample ^ Total_Cov_bases ^ Mean_Cov ^ Median_Cov ^ %_bases_>15 ^ %_bases_>30 ^ %_bases_>40 ^ %_bases_>50 ^ | ||
| | SGT038 | 1839178575 | 36.52 | 35 | 88.2 | 58.2 | 39.2 | 24.0 | | | SGT038 | 1839178575 | 36.52 | 35 | 88.2 | 58.2 | 39.2 | 24.0 | | ||
| | SGT077 | 1617599251 | 32.12 | 30 | 84.2 | 49.6 | 30.3 | 16.6 | | | SGT077 | 1617599251 | 32.12 | 30 | 84.2 | 49.6 | 30.3 | 16.6 | | ||
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| | SGT274 | 1822284846 | 36.18 | 34 | 88.0 | 58.1 | 38.8 | 23.4 | | | SGT274 | 1822284846 | 36.18 | 34 | 88.0 | 58.1 | 38.8 | 23.4 | | ||
| - | ===== CNAG's pipeline ===== | + | ==== CNAG's pipeline ==== |
| - | ^ Sample ^ Total_cov_bases ^ Mean_Cov ^ Median_Cov ^ %_bases_>15 ^ %_bases_>30 ^ %_bases_>40 ^ %_bases_>50 ^ | + | ^ Sample ^ Total_Cov_bases ^ Mean_Cov ^ Median_Cov ^ %_bases_>15 ^ %_bases_>30 ^ %_bases_>40 ^ %_bases_>50 ^ |
| | SGT038 | 3808950667 | 75.63 | 68 | 95.6 | 85.7 | 76.2 | 66.1 | | | SGT038 | 3808950667 | 75.63 | 68 | 95.6 | 85.7 | 76.2 | 66.1 | | ||
| | SGT077 | 3260149358 | 64.74 | 58 | 94.4 | 81.1 | 69.3 | 57.8 | | | SGT077 | 3260149358 | 64.74 | 58 | 94.4 | 81.1 | 69.3 | 57.8 | | ||
