Table 2 Distribution of Mean of total number of ROH (NROH) and total sums of ROH (SROH) per individual in BirThree dataset after implementing minimal ROH length threshold of 100 Kb, and 1.5 Mb, respectively
From: Profiling of runs of homozygosity from whole-genome sequence data in Japanese biobank
Tools | Regions and parameter options | ROH metrics | Mean values for different minimal ROH lengths | |
---|---|---|---|---|
>100 Kb | >1.5 Mb | |||
BCFtools | All variant sites | NROH | 1713 | 10.44 |
SROH | 505,931,167 | 27,486,031 | ||
Only SNP array-based sites*a | NROH | 67 | 7.71 | |
SROH | 61,110,307 | 22,104,265 | ||
PLINK | All variant sites/Het_1 | NROH | 2726 | 7.18 |
SROH | 627,622,136 | 20,846,395 | ||
All variant sites/Het_2 | NROH | 3072 | 10.88 | |
SROH | 758,579,183 | 29,116,852 | ||
All variant sites/Het_3 | NROH | 3324 | 14.16 | |
SROH | 848,691,286 | 36,505,896 | ||
All variant sites/Het_4 | NROH | 3532 | 16.82 | |
SROH | 919,263,432 | 42,598,045 | ||
Only SNP array-basedsites/Het_1*a | NROH | 357 | 11.06 | |
SROH | 206,508,058 | 27,499,818 |