Table 3.

Plastid variant call results from SAMtools mpileup versus GATK HaplotypeCaller using the purified cpDNA and the three total genomic DNA samples.

	SAMtools mpileup				GATK HaplotypeCaller
Aligned (ref)	Pt only		Pt and Mt		Pt only		Pt and Mt
Filter	Total	Pass	Total	Pass	Total	Pass	Total	Pass
Purified cpDNA	86	64	86	64	129	129	129	129
Total DNA_1	86	66	86	67	129	129	129	129
Total DNA_2	131	64	87	65	129	129	129	129
Total DNA_3	128	69	99	69	129	129	129	129

Processed reads were aligned on the plastid reference genome (Pt only) or on the combined plastid–mitochondrial reference genome (Pt and Mt). Heterozygous and low-quality variants (QUAL < 20) were filtered out in SAMtools, and low-quality variants (QUAL < 20) were filtered out in GATK.