Table 2.

Numbers of Y-chromosome bases, Y-SNPs and haplogroups retrieved

Sample	Condition	Positions recovered	Total SNPs	Ancestral SNPs	Derived SNPs	Haplogroup retrieved
STM1	All	2,205,331	12,061	11,625	436	R1b-M343
	Pre-capture	93,725	595	577	18	R1b-M343
	YCC	1,372,731	8103	7805	298	R1b-M343
	WGC	354,255	2414	2321	93	R1b-M343
	WGC + YCC	493,085	2971	2871	100	R1b-M343
STM2	All	428,846	2183	2091	92	E1b1a1a1-M80
	Pre-capture	19,994	109	100	9	E1b1a1a1-M80
	YCC	220,732	1262	1215	47	E1b1a1-M2
	WGC	109,411	760	726	34	E1b1a1a1-M80
	WGC + YCC	219,152	114	110	4	CT-M168
PI174	All	3224	19	18	1	A1-V168
	Pre-capture	129	0	0	0	–
	YCC	1993	12	11	1	A1-V168
	WGC	147	2	2	0	A1-V168
	WGC + YCC	1818	11	10	1	A1-V168
PI383	All	7738	46	45	1	P-M45
	Pre-capture	146	0	0	0	–
	YCC	1809	13	12	1	P-M45
	WGC	473	5	5	0	P-M45
	WGC + YCC	6890	42	41	1	P-M45
PI435	All	16,469	100	97	3	BT-M42
	Pre-capture	164	0	0	0	–
	YCC	1918	15	15	0	BT-M42
	WGC	2632	18	18	0	–
	WGC + YCC	12,399	86	83	3	BT-M42
PI437	All	3444	14	14	0	–
	Pre-capture	103	0	0	0	–
	YCC	938	6	6	0	–
	WGC	296	0	0	0	–
	WGC + YCC	2320	11	11	0	–