Table 3.

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

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

^aThe reliability of GBS genotypes was based on the reference calls generated using the SNP50 BeadChip. Estimation of the concordant SNPs is reported