Table 2.

Allele frequency and genomic features of the SNVs and indels identified in the CASPMI cohort

Type	AF	Exonic	Splicing	ncRNA exonic	ncRNA intronic	ncRNA splicing	5′UTR	3′UTR	Intronic	Up-stream	Down-stream	Intergenic	Total
SNV	≥50%	11,445	51	5749	105,509	32	2969	13,805	664,216	11,693	12,061	1,088,588	1,916,118
	5%–50%	23,613	65	11,660	199,759	67	6021	27,056	1,343,806	23,236	24,117	2,119,311	3,778,711
	0.5%–5%	25,422	115	8763	144,622	58	5977	24,531	1,025,511	18,148	18,337	1,492,106	2,763,590
	<0.5%	201,609	1595	51,408	872,202	280	41,586	157,899	6,221,982	113,756	109,551	8,619,679	16,391,547
	All	262,089	1826	77,580	1,322,092	437	56,553	223,291	9,255,515	166,833	164,066	13,319,684	24,849,966
Indel	≥50%	347	65	713	17,654	3	467	2778	114,668	2217	2400	173,161	314,473
	5%–50%	651	40	1813	52,435	9	935	7771	366,652	6798	7523	512,111	956,738
	0.5%–5%	1080	43	1594	41,482	13	1058	6936	289,865	5520	5684	393,381	746,656
	<0.5%	7940	458	5213	102,642	45	4264	21,859	702,803	14,524	14,846	958,744	1,833,338
	All	10,018	606	9333	214,213	70	6724	39,344	1,473,988	29,059	30,453	2,037,397	3,851,205

Note: SNV, single-nucleotide variant; AF, allele frequency.