Table 2.

Genomic and archaeological data for the six BA whole-genome sequenced individuals from this study

Archaeological site	Sample ID	Time period	Culturea	Age (cal BCE)	Shotgun DoC (all)b	Shotgun DoC (5 bp trim)b	Capture DoCc	Contam. mtDNA (%)d	Contam. X (%)e	Sex	mtDNA haplogroup	Y haplogroup
Manika	Mik15	EBA	Early Helladic	2890–2764	3.5	2.2	–	0.01–0.58	–	XX	J2b1	–
Petras	Pta08	EBA	Early Minoan	2849–2621	4.0	3.0	38.0	0.01–0.52	1.0–1.1	XY	H	G2-L156
Koufonisi	Kou01	EBA	Early Cycladic	2464–2349	2.6	2.0	42.9	0.02–0.97	0.6–0.8	XY	K1a2c	J2a-M410
	Kou03	EBA	Early Cycladic	2832–2578	2.8	2.2	–	0.18–1.49	–	XX	K1a	–
Logkas	Log02	MBA	Middle Helladic	1924–1831	4.3f	3.4	109.1	0.02–0.39	–	XX	H55a	–
	Log04	MBA	Middle Helladic	2007–1915	4.9	4.0	-	0.02–0.94	–	XX	J1c+16261	–

Details on the origin of the individuals, their cultural group, and their radiocarbon dates. ID: identifier; BCE: Before the Common Era; DoC: Depth of Coverage; 5 bp trim: 5 bp trimming; mtDNA: mitochondrial DNA; Contam.: Contaminaton;EBA: Early Bronze Age; MBA: Middle Bronze Age. See also Figures 1, S2, and S3, Tables 1 and S1, and STAR Methods.

^aTerminology of cultural groups.

^bDepth of Coverage (DoC) before (“all”) and after trimming 5 bp from the extremities of the reads (“5 bp trim”).

^cAverage number of reads covering the nuclear capture regions.

^d95% credible interval (STAR Methods).

^e95% confidence interval assuming a European population (HapMap CEU) as contaminant (Star Methods).

^fUSER-treated sample (STAR Methods).