Steps | Measured parameters | GBS | 3D-GBS |
---|---|---|---|
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/cMc | 3.7 | 2.3 |
Number of gaps > 10 cM | 7 | 10 | |
Number of gaps > 20 cM | 0 | 1 |