Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance

Table 2 Coverage of quartet benchmark regions on coding region and clinically related genes

Class	Total bases (bp)	Small variant benchmark regions of Quartet¹ v1.1 (%)	SV benchmark regions of Quartet D5&D6 v1.1 (%)	SV benchmark regions of Quartet-F7 v1.1 (%)	SV benchmark regions of Quartet-M8 v1.1 (%)
GRCh38 (chr1-22, X)	3,031,042,417	87.7	86.5	85.5	85.7
Gene	1,776,904,532	93.6	93.4	92.5	92.3
Exon	156,255,092	93.4	93.0	91.5	91.7
CDS	35,744,776	94.4	93.6	92.2	92.4
ClinVar	6,247,973	94.4	93.6	92.9	92.9

¹The benchmark regions of the four Quartet reference samples are the same
²Genomic regions of gene, exon and CDS (coding sequences) are extracted from gencode v43
³Genomic regions of variants of ClinVar are extracted from ClinVar v2023-06-17

ISSN: 1474-760X