Table 1 Sequencing and SNP-calling data generated from GBS and 3D-GBS libraries of 16 soybean samples

Sequencing

Mean read count (M)

0.6

0.6

Coverage (%)^a

4.7

1.2

Mean depth of coverage (X)^b

5.1

14.5

Mean mapping quality

41

42

SNP calling

SNP count

7904

4826

Proportion of missing data (%)

33.7

15.3

Proportion of heterozygous genotypes (%)

4.4

3.8

Average minor allele frequency (%)

33.8

31.3

Nucleotide diversity (p per bp)

0.43

0.42

Physical map

SNP/Mb

8.3

5.1

Number of gaps > 5 Mb

9

6

Number of gaps > 10 Mb

1

0

Genetic map

SNP/cM^c

3.7

2.3

Number of gaps > 10 cM

7

10

Number of gaps > 20 cM

0

1