Supplementary Table S1: Basic statistics of raw reads and results of read mapping and SNV calling using two pipelines
Sample ID	Raw Reads (Gb)	Mapping Ratio (%) by SOAP2	Identified SNVs by SOAPsnp	Mapping Ratio (%) by BWA	Identified SNVs by SAMtools
KPGP_00001	96.86	93.58	3,431,377	95.32	3,422,437
KPGP_00002	98.32	92.99	3,435,987	94.81	3,411,488
KPGP_00003	107.55	91.13	3,424,452	94.31	3,465,591
KPGP_00004	112.97	91.52	3,444,114	94.16	3,480,518
KPGP_00005	95.22	92.54	3,419,112	94.5	3,441,346
KPGP_00006	93.45	91.86	3,400,321	94.36	3,429,602
KPGP_00007	95.28	89.75	3,374,515	92.2	3,406,348
KPGP_00008	97.62	91.1	3,404,660	93.15	3,413,922
KPGP_00009	93.94	92.33	3,426,420	94.56	3,428,344
KPGP_00032	112.19	91.46	3,413,019	94.53	3,421,575
KPGP_00033	108.20	91.01	3,431,517	94.06	3,464,829
KPGP_00088	96.60	92.14	3,397,729	94.62	3,448,865
KPGP_00089	97.95	92.17	3,407,842	94.53	3,456,718
KPGP_00090	92.92	92.33	3,420,401	94.47	3,441,538
KPGP_00091	91.88	91.76	3,411,441	94.23	3,425,495
KPGP_00117	115.45	88.96	3,348,780	92.07	3,379,258
KPGP_00120	116.63	91.16	3,402,878	94	3,407,932
KPGP_00121	119.49	89.91	3,402,177	92.8	3,451,523
KPGP_00122	105.10	87.69	3,318,098	93.18	3,401,046
KPGP_00124	115.37	89.37	3,387,796	92.28	3,409,097
KPGP_00125	118.67	91.94	3,387,680	94.81	3,407,860
KPGP_00127	118.88	90.79	3,373,489	93.69	3,389,952
KPGP_00128	117.85	91.69	3,399,743	94.8	3,439,415
KPGP_00129	107.12	90.76	3,353,477	93.53	3,369,094
KPGP_00131	120.14	91.79	3,407,760	94.57	3,417,905
KPGP_00132	122.24	91.67	3,389,447	94.53	3,435,532
KPGP_00134	119.54	89.24	3,371,161	91.95	3,419,917
KPGP_00136	114.98	88.22	3,368,716	91.48	3,400,390
KPGP_00137	118.03	91.72	3,370,901	94.64	3,416,798
KPGP_00138	123.87	89.6	3,380,214	92.75	3,434,070
KPGP_00139	105.73	89.95	3,387,680	94.44	3,394,218
KPGP_00141	111.51	91.53	3,361,314	94.68	3,412,735
KPGP_00142	125.02	90.36	3,388,726	93.37	3,408,280
KPGP_00144	127.00	91.15	3,406,971	94.23	3,414,758
KPGP_00145	111.86	91.99	3,399,180	94.66	3,396,973
Union	3,825.45	91.05	9,964,511	93.89	9,119,633