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

Table 1 Summary of quartet small variant and structural variant benchmark calls and regions

		Quartet-D5	Quartet-D6	Quartet-F7	Quartet-M8
Small Variant Benchmark Calls	Total variants ^a	4,122,817	4,122,817	4,097,306	4,123,162
	SNV	3,558,056	3,558,056	3,527,544	3,557,613
	sINS ^b	274,854	274,854	273,186	276,426
	sDEL ^b	281,212	281,212	278,427	280,765
	Block substitutions ^c	8695	8695	8149	8258
	Het/Hom ratio	1.37	1.37	1.30	1.35
	SNV Ti/Tv	2.08	2.08	2.07	2.07
	Benchmark region, chr1-22, X(bp)	2,658,688,832	2,658,688,832	2,658,688,832	2,658,688,832
Structural Variants Benchmark Calls	Total variants ^d	15,005	15,005	15,098	14,893
	INS ^e < 1kb	7216	7216	7353	7161
	INS \(\ge\) 1kb	734	734	755	717
	DEL ^e< 1kb	6352	6352	6287	6324
	DEL \(\ge\) 1kb	703	703	703	691
	Het/Hom ratio	1.43	1.43	1.45	1.57
	Longest INS (bp)	12,450	12,450	12,450	12,450
	Longest DEL (bp)	117,310	117,310	435,343	494,712
	Affected bases (bp)	7,796,176	7,796,176	8,821,558	8,550,650
	Benchmark region, chr1-22 (bp)	2,622,728,511	2,622,728,511	2,591,967,148	2,596,140,552

^aAll small variants benchmark calls are located in small variants high-confidence region, and false positive variants detected by orthogonal validation have been removed
^bsINS and sDEL stand for short insertion and deletion with size less than 50 bp
^cBlock Substitutions are variants with length change between REF and ALT. It is not simple addition or removal of bases, for example, ATT -> CTTT
^dStructural variant benchmark calls include variants not located in benchmark regions
^eINS and DEL stand for long insertion and deletion with size over or equal to 50 bp

ISSN: 1474-760X