Sequencing quality control parameters, coverage and detected variants by targeted resequencing of the CFTR gene using pools of 8, 12, 16 and 24 samples
Samples | Pool name | All samples | 8A | 8B | 12A | 12B | 16A | 16B | 24A |
---|---|---|---|---|---|---|---|---|---|
Precapture pooling (number of samples) | All | 8 | 8 | 12 | 12 | 16 | 16 | 24 | |
Sequencing | QC-passed reads±%CV | 11701689±35 | 19187383±14 | 17639.073±20 | 8430967±15 | 11654345±15 | 8614519±10 | 10449749±30 | 11779102±26 |
% Mapped | 94.9 | 97.13 | 96.36 | 94.53 | 96.36 | 96.4 | 94.23 | 92.58 | |
% Properly paired | 92.98 | 96.03 | 95.05 | 92.49 | 95.06 | 95.04 | 92.07 | 89.73 | |
Coverage | Mean coverage (X)±%CV | 231±43 | 425±16 | 358±22 | 101±12 | 223±16 | 173±12 | 212±29 | 244±22 |
Mean coverage extended 150 bp (X)±%CV | 199±43 | 367±17 | 313±22 | 88±11 | 192±16 | 150±13 | 181±29 | 209±22 | |
% Enrichment | 55.31 | 58.54 | 57.12 | 43.29 | 55.8 | 56.42 | 56.67 | 57.75 | |
% target bases covered=0× | 0.07 | 0.03 | 0.01 | 0.12 | 0.1 | 0.09 | 0.07 | 0.06 | |
% target bases covered≥1× | 99.93 | 99.97 | 99.99 | 99.88 | 99.9 | 99.91 | 99.93 | 99.94 | |
% target bases covered≥5× | 99.7 | 99.84 | 99.86 | 99.41 | 99.72 | 99.76 | 99.67 | 99.72 | |
% target bases covered≥10× | 99.39 | 99.76 | 99.78 | 98.55 | 99.49 | 99.56 | 99.29 | 99.45 | |
% target bases covered≥20× | 98.48 | 99.63 | 99.58 | 95.92 | 98.82 | 98.92 | 98.23 | 98.69 | |
% target bases covered≥50× | 93.13 | 98.86 | 98.38 | 79.25 | 95.1 | 94.74 | 92.49 | 94.78 | |
% target bases covered≥100× | 78.53 | 96.34 | 93.79 | 43.14 | 83.23 | 77.56 | 78.29 | 83.64 | |
CFTR variants | SNVs | 115 | 124 | 89 | 121 | 119 | 124 | 121 | 104 |
Novel SNVs | 4 | 5 | 5 | 3 | 3 | 4 | 3 | 4 | |
Exonic SNVs | 3 | 2 | 2 | 3 | 3 | 3 | 3 | 2 | |
Missense, nonsense and splice site SNPs | 2 | 2 | 1 | 2 | 2 | 2 | 2 | 2 | |
InDels | 28 | 29 | 29 | 28 | 30 | 31 | 28 | 25 | |
Novel InDels | 19 | 19 | 19 | 19 | 20 | 21 | 17 | 16 | |
Frameshift and non-Frameshift InDels | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
CFTR, cystic fibrosis transmembrane regulator; CV, Coefficient of variation; InDels, insertions and deletions; SNV, single nucleotide variants; QC, Coefficient of variation.