Table 1

Numbers of LoF variants before and after filtering. Total numbers of candidate LoF variants and average number of LoF sites per individual (homozygous sites in parentheses) are shown for each LoF class. For large deletions, numbers represent total number of genes predicted to be inactivated.

Variant
type
Before filteringAfter filtering
Total1000G low-coverage
average per individual
NA12878Total1000G low-coverage
average per individual
NA12878
CEUCHB+JPTYRICEUCHB+JPTYRI
Stop111185.7 (21.8)113.4 (26.7)109.1 (23.7)115 (25)56526.2 (5.2)27.4
(6.9)
37.2 (6.3)23 (2)
Splice65880.5 (29.5)98.1 (35.6)89.0 (30.4)95 (32)26711.2 (1.9)13.2
(2.5)
13.7 (1.9)12 (1)
Frameshift
indel
1040217.8 (112.1)225.5 (121.7)247.2 (118.7)348 (159)33738.2 (9.2)36.2
(9.0)
44.0 (8.0)38 (11)
Large
deletion
14232.4 (12.2)31.2 (11.8)31.4 (9.7)31 (5)11628.3 (6.2)26.7
(5.9)
26.6 (5.5)24 (4)
Total2951416.4 (175.6)468.2 (195.8)476.7 (316.0)654 (286)1285103.9 (22.5)103.5 (24.3)121.5 (21.7)97 (18)