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Table 5 Comparative pipeline performances, in terms of consistency in genotyping biological replicates

From: GBS-SNP-CROP: a reference-optional pipeline for SNP discovery and plant germplasm characterization using variable length, paired-end genotyping-by-sequencing data

   cv. ‘Opitz Male’ cv. ‘Dumbarton Oaks’
Pipelines Number of SNPsa Gower genetic similarityb Pearson correlationc Shared genotype calls (%)d Gower genetic similarity Pearson correlation Shared genotype calls (%)
GBS-SNP-CROP-MR01 21,318 0.999 0.998 99.9 0.998 0.997 99.8
GBS-SNP-CROP-RG 5,471 0.999 0.998 99.9 0.998 0.997 99.9
TASSEL-UNEAK 1,160 0.935 0.948 93.6 0.950 0.961 94.8
TASSEL-GBS-32 bp 5,593 0.967 0.909 96.3 0.969 0.922 96.4
TASSEL-GBS-64 bp 8,907 0.967 0.920 96.7 0.966 0.919 96.6
  1. a The total number of SNPs used in this analysis refers to numbers from Table 4B
  2. b A modified Gower’s general Coefficient of Similarity [48], ranging from 0 to 1, to quantify identity-by-state based on bi-allelic SNPs
  3. c Pearson correlation calculated using R [31]; for all correlations in the table, p-value < 0.01
  4. d The percentage of SNPs with exact genotype matches for the two biological replicates. All loci with missing data for either replicate were discarded