Physical separation of haplotypes in dikaryons allows benchmarking of phasing accuracy in Nanopore and HiFi assemblies with Hi-C data

Table 4 Comparisons between the Nanopore and HiFi chromosomes as well as between the haplotypes of Pt76 and Pgt

	Comparison between Pt76 chromosomes		Comparison between HiFi-Canu Pt76 chromosomes		Comparison between Pgt chromosome assemblies
	HiFi-Canu	Nanopore	Haplotype A	Haplotype B	Haplotype A	Haplotype B
Number of sequences	36	36	18	18	18	18
Aligned bases	97.6%	99.1%	97.1%	98.9%	85.6%	89.5%
Unaligned bases	2.5%	0.9%	2.9%	1.1%	14.4%	10.5%
Average identity of 1-to-1 alignments	99.7%		99.5%		95.8%
Average identity of M-to-M alignments	99.7%		99.0%		95.4%
Translocations	963	1023	1161	1179	12,087	12,139
Inversions	51	49	163	174	537	566
Insertions	1732	3206	10,896	11,548	40,159	49,047
Tandem duplication insertion	12	64	329	346	86	121
Total SNPs	62,461		334,571		1,420,848
Total Indels	249,485		186,609		877,171

ISSN: 1474-760X