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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
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BMC Bioinformatics

ISSN: 1471-2105

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