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Table 4 Comparative pipeline performances before (4A) and after (4B) depth-based genotyping criteria and population-level SNP calling filters for 150 bp paired-end GBS data from 48 accessions of Actinidia arguta

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

Pipeline Number of SNPsa Average depth [D]b Reads with D ≥ 20 (%)c Hetero (%)d Homo (%)e Missing data (%)f
4A. No SNP calling or genotyping filters appliedg
 GBS-SNP-CROP-MR01 56,598 44.47 52.85 26.19 57.25 16.55
 GBS-SNP-CROP-RG 23,564 47.39 39.00 26.10 51.09 22.80
 TASSEL-UNEAK 12,905 6.98 9.61 13.93 52.12 33.94
 TASSEL-GBS-mxTagL32 19,095 134.18 49.20 16.86 71.66 11.46
 TASSEL-GBS-mxTagL64 25,005 34.65 35.60 19.21 65.80 14.98
4B. Depth-based genotyping criteria and population-level SNP calling filters appliedh
 GBS-SNP-CROP-MR01 21,318 69.34 99.92 34.51 56.85 8.64
 GBS-SNP-CROP-RG 5,471 77.11 99.85 38.31 53.29 8.40
 TASSEL-UNEAK 1,160 44.70 83.62 31.66 66.61 1.73
 TASSEL-GBS-mxTagL32 5,593 64.41 92.52 26.33 71.58 2.09
 TASSEL-GBS-mxTagL64 8,907 51.42 78.07 27.80 69.36 2.84
  1. a Total number of SNPs called within each pipeline, under the indicated SNP calling filters and genotyping criteria
  2. b Average read depth for all SNPs across the entire population
  3. c Percentage of called SNPs with an average read depth of at least 20
  4. d Percentage of heterozygous genotype calls
  5. e Percentage of homozygous genotype calls
  6. f Percentage of missing cells (i.e. no genotype call for a given SNP*accession combination)
  7. g Liberal pipeline results in the absence of subsequent SNP calling or genotyping filters
  8. h Pipeline results after culling SNPs with less than 75 % scored genotypes, with D ≤ 4 (low depth), or D ≥ 200 (over-represented sequences). Further reduction is due to imposing stringent depth-based genotyping criteria, including a minimum read depth of 11 for homozygotes when the secondary allele count is zero, a minimum depth of 48 for homozygotes when the secondary allele count is one, a minimum depth of 3 for each allele for heterozygotes, and a read-depth ratio of the lower- to higher-depth allele greater than 0.1