Detection and validation of structural variations in bovine whole-genome sequence data

Table 10 Proportion of structural variants in LINE regions, compared with the genome as a whole and other regions

Sample set	Non-L1_exon	L1	Fold_change	t test p value
Deletions				0.003538
FAM_HOL	0.000805	0.003322	4.124097
FAM_JER	0.000139	0.000818	5.893840
POP_HOL	0.002868	0.005747	2.003659
POP_JER	0.001654	0.004282	2.588642
VAL_SV	0.001384	0.004992	3.608023
Insertions				0.185507
FAM_HOL	0.000001	0.000000	0.000000
FAM_JER	0.000000	0.000000	0.000000
POP_HOL	0.000249	0.000196	0.787844
POP_JER	0.000000	0.000000	0.000000
VAL_SV	0.000003	0.000003	1.080158
Inversions				0.260667
FAM_HOL	0.000084	0.000040	0.479628
FAM_JER	0.000010	0.000005	0.484786
POP_HOL	0.005262	0.005435	1.032979
POP_JER	0.000395	0.000437	1.106285
VAL_SV	0.000152	0.000123	0.810684
Duplications				0.082899
FAM_HOL	0.000122	0.000115	0.945850
FAM_JER	0.000016	0.000033	2.100240
POP_HOL	0.001611	0.002144	1.331104
POP_JER	0.000828	0.001416	1.710535
VAL_SV	0.000148	0.000164	1.103813

Fold change is equal to the percentage of the genome that harbors SV in the L1 regions divided by the percentage of the genome that harbors SV in the other regions

ISSN: 1297-9686