Table 1. Summary of the variants found in this study and their validation rate.

We have divided the variants into the heterochromatic region and the combined ampliconic and X-degenerate regions and into whether they occur in more than one haplogroup. The number of variants and the percentage of these that are already known (in parenthesis). The in silico concordance rate is how often an alternative variant found in one member of a family is found in the other member.

	Heterochromatic (0.9 Mb called)		ampliconic and X-degenerate (11.6 Mb called)
	Recurrent mutations	Non recurrent mutations	Recurrent mutations	Non recurrent mutations
SNPs	7415 (35.7%)	5113 (33.1%)	1730 (31.7%)	5785 (28.0%)
Deletions	295 (21.0%)	204 (17.7%)	569 (17.1%)	651 (20.0%)
Insertions	236 (22.9%)	184 (13.6%)	298 (10.4%)	609 (21.4%)
Complex	0	0	53 (5.6%)	74 (2.7%)
STRs	510 (12.2%)	383 (14.4%)	490 (29.6%)	798 (24.1%)
In silico validation rate
SNPs	0.65	0.99	0.59	0.99
Deletions	0.61	0.99	0.43	0.92
Insertions	0.64	0.99	0.61	0.97
Complex	NA	NA	0.60	0.94
STRs	0.69	0.99	0.69	0.98