Extended data Table 2:

Overview of repeat content (Mbp and percentage) in the ape genomes

	Human		Chimpanzee		Bonobo		Gorilla		Sumatran orangutan		Bornean orangutan		Siamang
	Mbp	%	Mbp	%	Mbp	%	Mbp	%	Mbp	%	Mbp	%	Mbp	%
DNA	108.59	3.48	110.60	3.48	110.74	3.47	111.82	3.15	111.20	3.41	110.83	3.44	106.76	3.27
LINE	633.55	20.33	636.62	20.04	638.42	19.99	649.75	18.33	686.42	21.06	683.56	21.22	631.83	19.37
PLE	0.06	0.00	0.07	0.00	0.07	0.00	0.07	0.00	0.07	0.00	0.07	0.00	0.07	0.00
LTR	272.91	8.75	274.90	8.65	275.67	8.63	277.85	7.84	279.36	8.57	278.28	8.64	256.49	7.86
SINE	393.51	12.62	391.01	12.30	393.08	12.3	397.19	11.20	396.85	12.17	395.47	12.28	402.73	12.34
RC	0.45	0.01	0.46	0.01	0.46	0.01	0.46	0.01	0.46	0.01	0.46	0.01	0.44	0.01
Retroposon	4.31	0.14	4.78	0.15	4.90	0.15	5.21	0.15	3.87	0.12	4.39	0.14	6.66	0.20
Satellite	161.77	5.19	251.68	7.92	270.19	8.46	462.50	13.04	191.45	5.87	159.20	4.94	376.70	11.55
Simple/low	108.38	3.48	69.17	2.18	107.68	3.37	181.36	5.11	134.09	4.11	138.98	4.31	54.29	1.66
Other	5.34	0.17	2.21	0.07	2.61	0.08	2.15	0.06	2.23	0.07	2.35	0.07	1.34	0.04
RNA	2.78	0.09	1.55	0.05	1.53	0.05	1.38	0.04	1.89	0.06	1.59	0.05	1.36	0.04
Un-masked	1,434.70	46.02	1,434.70	45.15	1,389.24	43.49	1,456.09	41.06	1,451.97	44.54	1,445.75	44.89	1,424.20	43.65
Total masked	1,691.65	54.27	1,743.04	54.85	1,805.35	56.51	2,089.74	58.94	1,807.88	55.46	1,775.19	55.11	1,838.69	56.35
NUMT	0.64	0.021	0.79	0.025	0.87	0.027	0.63	0.018	0.76	0.024	0.84	0.026	0.52	0.016