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Table 2 GBS calls relative to Sequenom MassARRAY genotypesa

From: Low-depth genotyping-by-sequencing (GBS) in a bovine population: strategies to maximize the selection of high quality genotypes and the accuracy of imputation

Conventional-primer method  
  Concordant Discordant Concordance (%)b
Chr Position Ref Alt MMb Mmb mmb MM Mm mm  
5 124968560 C T 0 11 5 0 0 0
6 120556623 T C 1 8 0 0 0 0
7 25377202 A G 0 2 1 0 0 0
12 81073590 G T 5 4 0 0 0 0
17 4536929 G A 2 8 0 0 0 0
18 11257808 A G 2 8 0 0 0 0
18 63490716 C T 6 17 0 0 0 0
23 18485367 C G 2 8 0 0 0 0
28 1121069 G T 5 5 0 0 0 0
  Total 23 71 6 0 0 0 100.0
Selective-primer method
5 124968560 C T 3 13 16 0 9 0  
6 120556623 T C 10 22 12 0 2 0
7 25377202 A G 5 17 19 0 1 1
11 6123151 T C 18 13 3 0 8 0
12 81073590 G T 19 11 3 0 7 0
17 4536929 G A 11 11 12 0 9 0
18 11257808 A G 20 16 6 0 3 0
18 63490716 C T 17 13 4 0 7 0
23 18485367 C G 18 13 2 0 4 0
24 26394985 G T 18 13 7 0 5 0
24 26395035 C T 7 14 18 0 6 0
28 1121069 G T 24 9 0 0 6 0
X 49928152 C T 34 8 0 0 0 0
  Total 204 173 102 0 68 0 87.6
  1. aThe 13 single-nucleotide polymorphisms (SNPs) examined were initially detected in a selective-primer dataset. Only 9 of these 13 SNPs could be retrieved in the corresponding conventional-primer dataset. Variants in these datasets were kept if they qualified based on a read depth ≥ 5, a genotype quality score ≥ 20, no more than one alternative allele, a call rate > 0.2, and a minor allele frequency ≥ 0.025. Chr: chromosome; Ref: reference allele; Alt: alternate allele; MM: homozygous for the reference allele; Mm: heterozygous; mm: homozygous for the alternate allele
  2. bThe reliability of SNP prediction was based on the reference calls predicted using the Sequenom MassARRAY technology. Discordant SNP reports call conflict by GBS