Table 2.

Estimated numbers of potentially functional variants in genes.

	Combined	Combined	Low Coverage		High-Coverage Trio		Exon Capture
class	Total	Novel	Total	Individual*	Total	Individual*	Total	Individual*	GENCODE extrap.
synonymous SNPs	60157	23498	55217	10572-12126	21410	9193-12500	5708	461-532	11553-13333
nonsynonymous SNPs	68300	34161	61284	9966-10819	19824	8299-10866	7063	396-441	9924-11052
small in-frame indels	714	383	666	198-205	289	130-178	20	1-3	~50-100
stop losses	77	40	71	9-11	22	4-14	6	0-0	~0
stop-introducing SNPs	1057	755	951	88-101	192	67-100	82	2-3	~50-75
splice-site-disrupting SNPs	517	399	500	41-49	82	28-45	3	1-1	~50
small frameshift indels	954	551	890	227-242	433	192-280	2	0	~0
genes disrupted by large deletions	147	71	143	28-36	82	33-49	NA	NA	NA
total genes containing LOF variants	2304	NA	1795	272-297	483	240-345	77	2-3	~50-75
HGMD "damaging mutation" SNPs	671	NA	578	57-80	161	48-82	99	2-4	~50-100

^*Interquartile range of number of SNPs per individual.