Table 1.

Overview of nonsyntenic and previously unresolved regions and their respective variant counts.

	Nonsyntenic	Previously unresolved
Summary
Total span (bp) (excluding Ns)	240,044,315 (228,569,315)	189,036,735 (177,561,735)
Unique span (100mers)	65,471,195	40,205,401
Protein-coding genes	207	207
Entire region
1KGP SNVs + indels (within genes)	3,692,439 (138,829)	2,370,384 (52,567)
Short-read SNVs per sample	65,931 to 101,161	35,506 to 56,489
Long-read SNVs per sample	1,178,371 to 1,467,243	957,629 to 1,197,463
Short-read SNVs confirmed by long reads	73 to 78%	64 to 69%
Long-read SNVs identified in short reads	4 to 5%	3%
SNVs concordant between long reads	41 to 43%	38 to 40%
High-confidence regions (excluding coverage abnormalities)
High-confidence region bases	13,683,528	2,987,935
Short-read SNVs confirmed by long reads in high-confidence regions	95 to 96%	84 to 88%
Long-read SNVs identified in short reads in high-confidence regions	60 to 63%	39 to 46%
SNVs concordant between long reads in high-confidence regions	91 to 95%	81 to 90%