Table 2 Variant calling using different subsets of reads derived from 3D-GBS on 16 soybean samples

Sequencing

Coverage (%)^a

0.6

0.7

0.9

1

Mean depth of coverage (X)^b

2.7

4.1

6.3

8.4

SNP calling

SNP count

1,314

2,299

3,587

4,082

Proportion of missing data (%)

37.1

29.3

23.3

20.3

Proportion of heterozygous genotypes (%)

6.1

5.2

5

4.6

Average minor allele frequency (%)

27.3

27.2

26.2

25.9

Nucleotide diversity (p per bp)

0.36

0.36

0.35

0.35

Physical map

SNP/Mb

1.4

2.4

3.8

4.3

Number of gaps > 5 Mb

23

9

5

7

Number of gaps > 10 Mb

6

1

1

0

Genetic map

SNP/cM^c

0.6

1.1

1.7

2

Number of gaps > 10 cM

29

18

12

9

Number of gaps > 20 cM

2

1

1

1