Table of Contents
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 |
