Table 1. Concordance values for samples passing both quality check values.

Samples passing QC	Whole exome		Whole genome
	Nr. of alleles typed	Concordance%	Nr. of alleles typed	Concordance%
HLA-A	340	92.3	52	78.9
HLA-B	360	96.7	60	85.0
HLA-C	322	92.6	24	95.8
All the genes	1022	93.9	136	84.6

Quality check (QC) was applied in these subsequent steps: i) only those samples were processed where the length of the read was longer than 76 bps for both ends ii) after alignment the percentage of the covered region () was calculated for exons 2 and 3. If any of these exons were covered by reads only less than 70% of the extent of the exon, the sample failed QC and was discarded. iii) finally, using this formerly calculated value, if the average for exons 2 and 3 was less than 80%, the sample was discarded. Average coverage depth was not considered since was a better indicator of correct concordance.