Table 1.

Summary of NGS samples and aligned results.

	Library			Reads (After_QC)			Aligned reads
DNA	SRA	Instrument	Layout	Read1	Read2	# Reads	# pt	# pt_uniq	% pt
Purified cpDNA	This study	Miseq	Paired	204	146	4,105,152	3,233,842	3,230,265	78.8
Total DNA_1	SRR1239746	Hiseq2000	Paired	90	89	10,595,500	1,076,775	1,003,940	10.2
Total DNA_2	SRR1614244	Hiseq2000	Paired	101	101	70,075,112	927,471	898,850	1.3
Total DNA_3	SRR077421	GAII	Paired	76	76	55,180,822	673,954	648,676	1.2
	SRR077422
	SRR077425

Purified cpDNA: Nipponbare cpDNA obtained by LN method (Figures 2A,B, column 4). Total DNAs: published Nipponbare whole-genome sequencing reads downloaded from public database. Reads 1 and 2 indicate mean lengths of reads.