Towards a comprehensive structural variation map of an individual human genome

Table 1 Structural variants detected by different methods

Method	Type	Number	Minimum size (bp)	Median size (bp)	Maximum size (bp)	Total size (bp)
Assembly comparison ^a	Homo. insertion	275,512	1	2	82,711	3,117,039
	Homo. deletion	283,961	1	2	18,484	2,820,823
	Hetero. insertion	136,792	1	1	321	336,374
	Hetero. deletion	99,814	1	1	349	250,300
	Inversion	88	102	1,602	686,721	1,627,871
Mate-pair	Insertion	780	346	3,588	28,344	3,880,544
	Deletion	1,494	340	3,611	1,669,696	10,531,345
	Inversion	105	368	3,121	2,026,495	8,068,541
Split-read	Insertion	8,511	11	16	414	224,022
	Deletion	11,659	11	18	111,714	1,764,522
Agilent 24 M	Duplication	194	445	1,274	113,465	1,065,617
	Deletion	319	439	1,198	852,404	2,779,880
NimbleGen 42 M	Duplication	366	448	4,665	836,362	11,292,451
	Deletion	358	459	2,460	359,736	3,861,282
Affymetrix 6.0	Duplication	17	8,638	42,798	640,474	2,011,557
	Deletion	21	2,280	13,145	856,671	1,978,028
Illumina 1 M	Duplication	3	11,539	22,148	87,670	121,357
	Deletion	9	8,576	32,199	145,662	431,131
Custom Agilent 244 k	Duplication	44	219	1,356	8,737	98,529
	Deletion	7	170	332	2,258	4,130
Non-redundant total ^b	Insertion/duplication	417,206	1	1	836,362	19,981,062
	Deletion	390,973	1	2	1,669,696	19,539,369
	Inversion	167	102	1,249	2,026,495	9,257,035

^aWe used an italicized font to distinguish the results from the Levy et al. [1] study. Moreover, from that previous study, we included all homozygous indels, heterozygous indels, indels embedded within simple, bi-allelic, and non-ambiguously mapped heterozygous mixed sequence variants, and only those inversions whose size is at most 3 Mb. ^bComplete data are presented in Additional files 19, 20 and 21. Non-redundant variation size distribution is presented in Figure 2a.

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