Table 2.

Variant calling metrics of Illumina PCR-free paired-end reads against the assemblies and Illumina PCR-free paired-end reads from Col-0 mapped against the TAIR10 reference assembly

Name	Round (#)	Total variants (#)	SNPs (#)	Insertions (#)	Deletions (#)
ONTcan	0	2,505,080	281,421	2,202,363	21,296
ONTcan	1	1,782,042	276,025	1,432,415	73,602
ONTcan	2	1,723,244	266,625	1,384,435	72,184
ONTcan	3	1,706,676	264,720	1,369,595	72,361
ONTcan	4	99,252	73,616	10,244	15,392
ONTmin	0	7,208,897	3,359,123	2,911,987	937,787
ONTmin	1	1,994,370	345,671	1,532,261	116,438
ONTmin	2	1,767,580	287,706	1,393,680	86,194
ONTmin	3	1,730,743	278,301	1,369,470	82,972
ONTmin	4	91,544	67,062	9026	15,456
PBfal	0	474,355	62,063	367,338	44,954
PBfal	1	39,433	26,486	6860	6087
PBfal	4	27,312	24,744	1010	1558
TAIR10	–	16,807	13,336	1770	1121

Assembly types: Oxford Nanopore MinION, ONT; PacBio Sequel, PacBio; Miniasm, min; Falcon, fal; Canu, can; reference genome, TAIR10. Polishing rounds PBfal: 0 = raw assembly; 1, arrow 1x; 4, pilon 1x