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

  1. PLINK “--homozyg-window-het” option values were set to a range of 1–4, i.e., allowing from one to four heterozygous calls per window. These are abbreviated as “Het_1”, “Het_2”, “Het_3”, and “Het_4”, respectively
  2. *a Although the SNP array data is unavailable, we have effectively trimmed whole genome sequencing (WGS) data to restrict our analysis exclusively on the regions specified by OmniExpressExome Array