Table 1. A census of insertion and deletion in CHM1.

The statistics of insertion and deletion events in CHM1 compared to GRCh37 are listed by sequence category. Low complexity sequence is divided between STR and VNTR (Supplementary Information). AluY, L1HS, SVA, and HERV are active mobile elements. Alu indel events in conjunction with STR sequences or mosaic Alu are considered separate from solitary AluY MEI. Inactive MEI include L1P, and AluS mobile elements. Rarely observed elements (<10) are combined as other. Classes of structural variation showing an insertional bias (>2.5 fold excess in CHM1) are shaded.

Structural variation between CHM1 and GRCh37.

	Insertion			Deletion			Ins/Del
	Number	Mean length	Total bases	Number	Mean length	Total bases	Total events	Total bases
STR >10bp	6,007	295	1,771,948	2,986	90	268,075	2.01	6.61
STR >= 50 bp	4,289	398	1,706,524	1,530	139	212,957	2.80	8.01
STR >10, < 50bp	1,718	38	65,424	1,456	38	5,518	1.18	11.86
Tandem Repeat	2,760	303	836,474	2,398	182	4,361,598	1.15	0.19
MEI	2,149	497	1,200,647	2,084	428	841,617	1.03	1.43
AluY	859	302	259,810	859	302	259,220	1.00	1.00
LINE/L1HS	145	2,412	349,780	141	2,411	339,971	1.03	1.03
SVA	457	369	168,762	382	274	104,589	1.20	1.61
HERV	58	338	19,619	60	180	10,779	0.97	1.82
Alu+STR/Alu+mosaic	287	413	118,486	186	262	46,905	1.54	2.53
Inactive	343	226	77,602	456	176	80,153	0.75	0.97
Centromeric satellites	669	693	463,687	817	722	590,223	0.82	0.79
HSAT	46	861	39,604	48	790	37,935	0.96	1.04
ALR	622	681	423,453	769	718	552,288	0.81	0.77
Other	168	112	18,790	277	98	27,144	0.61	0.69
Complex	1,115	1,927	2,148,642	317	2,066	654,834	3.52	3.28
Unannotated	2,386	60	143,598	2,313	62	143,559	1.03	1.00
Total	17,851	398	7,112,381	11,819	271	3,208,633	1.51	2.22
Euchromatic subtotal	15,776	390	6,149,335	10,303	248	2,559,644	1.53	2.40
Euchromatic subtotal (>=50 bp)	9,638	542	5,237,445	6,111	358	2,189,837	1.58	2.39