Table 1

Sequencing quality control parameters, coverage and detected variants by targeted resequencing of the CFTR gene using pools of 8, 12, 16 and 24 samples

SamplesPool nameAll samples8A8B12A12B16A16B24A
Precapture pooling (number of samples)All881212161624
SequencingQC-passed reads±%CV11701689±3519187383±1417639.073±208430967±1511654345±158614519±1010449749±3011779102±26
% Mapped94.997.1396.3694.5396.3696.494.2392.58
% Properly paired92.9896.0395.0592.4995.0695.0492.0789.73
CoverageMean coverage (X)±%CV231±43425±16358±22101±12223±16173±12212±29244±22
Mean coverage extended 150 bp (X)±%CV199±43367±17313±2288±11192±16150±13181±29209±22
% Enrichment55.3158.5457.1243.2955.856.4256.6757.75
% target bases covered=0×0.070.030.010.120.10.090.070.06
% target bases covered≥1×99.9399.9799.9999.8899.999.9199.9399.94
% target bases covered≥5×99.799.8499.8699.4199.7299.7699.6799.72
% target bases covered≥10×99.3999.7699.7898.5599.4999.5699.2999.45
% target bases covered≥20×98.4899.6399.5895.9298.8298.9298.2398.69
% target bases covered≥50×93.1398.8698.3879.2595.194.7492.4994.78
% target bases covered≥100×78.5396.3493.7943.1483.2377.5678.2983.64
CFTR variantsSNVs11512489121119124121104
Novel SNVs45533434
Exonic SNVs32233332
Missense, nonsense and splice site SNPs22122222
InDels2829292830312825
Novel InDels1919191920211716
Frameshift and non-Frameshift InDels11111111
  • CFTR, cystic fibrosis transmembrane regulator; CV, Coefficient of variation; InDels, insertions and deletions; SNV, single nucleotide variants; QC, Coefficient of variation.