Table 2.

Gorilla genome structural variants. Contigs greater than 200 kbp were mapped to GRCh38 by using BLASR (30). Nonrepetitive sequences contained at most 70% of sequence annotated as repeat by RepeatMasker (3.3.0) (28) or Tandem Repeats Finder 4.07b (29). Mosaic repeats are defined as one or more different repeat annotations; however, mosaic structural variants composed solely of Alu are listed separately because of their frequency.

	Insertion					Deletion
Repeat element	Count	Fixed	Average length (bp)	Standard deviation length (bp)	Total bases	Count	Fixed	Average length (bp)	Standard deviation length (bp)	Total bases
Complex, not repetitive	15,383	13,190	709.31	1807.29	10911284	13,749	10,250	763.17	1,954	10492765
Complex, repetitive	7,552	7,243	2716.96	2746.63	20,518,484	7,450	5,934	2757.39	2906.61	20,542,529
AluY	6,418	5,878	284.36	65.2	1,825,012	9,422	7,882	294.58	60.04	2,775,515
AluS	990	950	160.64	85.98	159,036	1,053	845	159.84	82.05	168,315
L1Hs	86	50	262.67	582.37	22,590	220	179	235.51	358.93	51,813
L1	1,339	1,256	438.5	737.1	587,147	1,181	874	450.84	744.1	532,441
L1P	1,891	1,660	278.26	487.86	526,192	1,430	1,098	312.81	493.88	447,317
SVA	1,498	1,097	1561.2	1007.55	2,338,672	1,194	786	1279.32	914.18	1,527,511
HERV	324	285	241.06	498.09	78,104	260	194	362.79	797.4	94,325
PTERV	190	179	2973.22	3427	564,912	1	1	188	0	188
Mosaic-Alu	1,433	1,355	320.11	262.59	458,717	1,514	1,177	307.92	260.53	466,194
STR	11,049	4,152	228.73	313.35	2,527,257	10,564	4,573	156.93	175.96	1,657,802
Tandem Repeats	7,351	4,520	367.74	811.03	2,703,261	7,828	4,225	323.38	558.5	2,531,424
Satellite	1,757	1,613	437.46	1072.08	768,617	1,768	1,437	426.73	1047.71	754,455
Other	1,319	1,184	201.01	247.8	265,130	1,196	896	180.49	227.79	215,872
Not base-pair resolved	41	N/A	49,496	23817.46	2029323	61	N/A	55,971	43,496	3,414,209
Total	58,621	44,653	789.54	2183.43	46,283,738	58,891	40,482	775.55	2804.21	45,672,675