espinos:results.coverage.analysis [Bier Wiki]

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====== 2.2 Coverage Analysis - All exome coverage ======

Here, we show an overview of all exome coverage obtained after processing reads in each pipeline. Main statistical indicators included in each table:

  * **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


==== BIER's pipeline ====

^  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  |
|  SGT077  |  1617599251  |  32.12  |  30  |  84.2  |  49.6  |  30.3  |  16.6  |
|  SGT161  |  1634278064  |  32.45  |  31  |  84.5  |  50.6  |  31.1  |  17.1  |
|  SGT187  |  1738854865  |  34.53  |  33  |  86.8  |  55.0  |  35.4  |  20.4  |
|  SGT230  |  1824828765  |  36.24  |  35  |  88.2  |  58.1  |  38.8  |  23.5  |
|  SGT238  |  1750563070  |  34.76  |  33  |  86.8  |  55.0  |  35.7  |  21.0  |
|  SGT241  |  1762155688  |  34.99  |  33  |  87.2  |  55.9  |  36.4  |  21.3  |
|  SGT274  |  1822284846  |  36.18  |  34  |  88.0  |  58.1  |  38.8  |  23.4  |

==== CNAG's pipeline ====

^  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  |
|  SGT077  |  3260149358  |  64.74  |  58  |  94.4  |  81.1  |  69.3  |  57.8  |
|  SGT161  |  3304555971  |  65.62  |  59  |  94.5  |  81.4  |  70.1  |  58.9  |
|  SGT187  |  3555029282  |  70.59  |  64  |  95.2  |  84.2  |  73.8  |  63.2  |
|  SGT230  |  3768806588  |  74.84  |  67  |  95.5  |  85.6  |  76.1  |  66.1  |
|  SGT238  |  3592296890  |  71.33  |  64  |  95.2  |  84.0  |  73.8  |  63.2  |
|  SGT241  |  3616180144  |  71.81  |  65  |  95.3  |  84.5  |  74.4  |  64.0  |
|  SGT274  |  3769591968  |  74.85  |  68  |  95.4  |  85.5  |  76.1  |  66.1  |

espinos/results.coverage.analysis.txt · Last modified: 2015/08/12 11:05 by cespinos

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