Table 2.

VCF statistics from variant calling software analysis.

Sample	SRA accession	Software/platform	Variant caller	SNVs	Indels	MNVs	Other	Ts/Tv
HG001	ERR1905890	Illumina	DRAGEN	41,633	3748	0	45,114	2.56
		CLC	Unknown	41,602	3865	484	54	2.57
		Partek	GATK	43,112	4314	0	12	2.48
			Freebayes + Samtools	42,843	4642	950	183	2.46
		Varsome	GATK	42,950	3887	0	0	2.51
HG002	SRR2962669	Illumina	DRAGEN	41,725	3719	0	45,235	2.56
		CLC	Unknown	41,693	3656	449	51	2.57
		Partek	GATK	42,979	4084	0	7	2.51
			Freebayes + Samtools	42,763	5509	925	160	2.48
		Varsome	GATK	42,816	3611	0	0	2.52
HG003	SRR2962692	Illumina	DRAGEN	41,659	3683	0	45,134	2.54
		CLC	Unknown	41,554	3597	465	51	2.54
		Partek	GATK	43,132	4063	0	8	2.48
			Freebayes + Samtools	42,624	5521	991	173	2.46
		Varsome	GATK	42,831	3503	0	0	2.5

SNV, single nucleotide variant; Indels, insertion or deletion; MNV, multi-nucleotide variant; ts/tv, transition-transversion ratio.