Table 2.

Descriptive statistics for certain genomic areas of the JPT sample: number of SNPs, percentage monomorphic markers, percentage significant markers in a HW exact test with $\mathit{\alpha }=0.001$, percentage of significant markers due to heterozygote excess and medians of the inbreeding coefficient (f) and the median read depth (DP)

	#SNPs	%Mono	%Sig	%HetExc	Med (f)	Med (DP)
CHR 6	5,008,031	83.87	1.26	22.29	−0.005	17,811
MHC	136,176	59.56	11.86	1.38	−0.005	16,917
Outside MHC	4,871,855	84.55	0.49	59.58	−0.006	17,854
HLA-A	348	37.36	1.83	50.00	−0.005	15,622
HLA-B	308	37.99	2.62	60.00	−0.002	10,426
HLA-C	329	44.68	5.49	90.00	0.016	13,691
HLA-DPA1	943	54.29	0.46	0.00	0.207	18,285
HLA-DPB1	763	44.95	6.19	0.00	0.142	17,937
HLA-DQA1	869	9.21	22.69	0.00	0.121	11,898
HLA-DQB1	905	6.52	30.14	0.00	0.142	10,915
HLA-DRB1	837	8.96	26.12	5.53	0.135	11,396
HLA-DRA	162	54.32	0.00	0.00	−0.010	19,879
CHR 21	1,102,563	84.54	1.62	80.06	−0.005	17,734
CHR 21 p.arm	23,453	85.57	36.04	85.25	−0.035	40,683
CHR 21 q.arm	1,072,796	84.54	0.56	60.02	−0.005	17,662
CHR 1-(Cen)	16,761	0.00	9.67	82.60	−0.010	19,402
CHR 1-outside	6,434,666	85.19	0.54	73.41	−0.007	18,017
CHR 2-(Cen)	8962	0.00	4.71	84.83	−0.005	18,816
CHR 2-outside	7,054,536	85.61	0.45	61.97	−0.005	17,948
CHR 3-(Cen)	17,114	0.00	0.62	94.34	−0.005	17,224
CHR 3-outside	5,800,292	85.23	0.48	53.68	−0.006	17,959
CHR 4-(Cen)	9621	0.00	4.77	89.98	−0.005	19,050
CHR 4-outside	5,708,252	84.88	0.49	53.58	−0.006	17,509
CHR 4 (4pTel)	4734	87.11	8.03	100.00	−0.020	18,861
CHR 10 (10pTel)	3704	87.53	5.19	0.00	−0.012	17,610
CHR 12 (12pTel)	2163	85.71	24.92	100.00	−0.020	28,209
CHR 14 (14pTel)	11,094	91.47	8.56	64.20	−0.005	22,173
Autosomes	80,931,043	85.01	0.62	58.93	−0.007	17,889