Table 1. Individual variant discovery in 1,005 unrelated Qatari¹.

Statistic	Genome (n=88)					51 Mb Exome (n=853)				38 Mb Exome (n=64)
	Individual	Autosomes	ChrX	ChrY	MtDNA	Individual	Autosomes	ChrX	ChrY	Individual	Autosomes	ChrX	ChrY
Variant sites	4,045,064	3,893,076	151,017	937	34	15,382	15,069	312	1	13,839	13,538	300	1
Novel variant sites	96,774	77,366	19,359	42	7	159	152	7	0	96	91	5	0
Novel variant rate	2.39%	1.99%	12.82%	4.48%	20.59%	1.03%	0.99%	2.24%	0.00%	0.69%	0.67%	1.67%	0.00%
Alternate alleles	5,510,301	5,311,794	196,565	1,874	68	21,046	20,613	431	2	19,116	18,709	405	2
Novel alternate alleles	98,792	78,916	19,778	84	14	160	153	7	0	97	92	5	0
Novel allele rate	1.79%	1.49%	10.06%	4.48%	20.59%	0.76%	0.74%	1.62%	0.00%	0.50%	0.49%	1.23%	0.00%
Heterozygous sites	2,594,268	2,489,084	105,184	—	—	9,759	9,564	195	—	8,897	8,698	199	—
Novel heterozygous sites	94,762	75,772	18,990	—	—	157	150	7	—	94	89	5	—
Novel heterozygous rate	3.65%	3.04%	18.05%	—	—	1.61%	1.57%	3.59%	—	1.06%	1.02%	2.51%	—
Mean depth at variant site	41	41	40	20	250	63	64	69	42	64	64	74	27
Mean depth at novel variant site	41	41	39	20	250	59	60	60	47	63	63	76	—
Transition:transversion ratio	2.03	2.03	1.78	1.51	33.00	3.18	3.18	2.77	—	3.25	3.26	2.67	—
Novel transition:transversion ratio	1.33	1.35	1.09	1.63	—	0.77	0.77	0.75	—	1.58	1.56	1.50	—

Shown is a summary of the average number of variants observed per individual, identified in 917 unrelated Qatari exomes and 88 unrelated Qatari genomes. Variants were genotyped separately for autosomes, X in males, X in females, Y in males and mtDNA; 99.8% of X variants in males were also observed in females, hence summary statistics are based on female chromosomes. Shown is the average per individual of number of variant sites, number of variant alleles, the transition-to-transversion ratio (Ts:Tv) of variants and the % not in dbSNP (novel).