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Table 3 Effect of read-depth and genotype quality (GQ) thresholds on the accuracy of GBS genotype calls

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

Dataset ID Filtering criteria (first step) Number of variants Markers shared with SNP50 Number of calls examined Estimated accuracy (%)a
1 ≥3 reads 182,334 1150 20,845 92.8
2 ≥3 reads and GQ > 20 154,991 1006 11,029 97.4
3 ≥4 reads 146,936 956 14,552 95.3
4 ≥4 reads and GQ > 20 130,813 865 8873 98.3
5 ≥5 reads 122,234 825 9818 97.0
6 ≥5 reads and GQ > 20 114,588 778 6952 98.8
7 ≥6 reads 105,085 723 6478 97.7
8 ≥6 reads and GQ > 20 101,552 689 5147 99.0
  1. aThe reliability of GBS genotypes was based on the reference calls generated using the SNP50 BeadChip. Estimation of the concordant SNPs is reported