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Table 2 Helianthus SNP filtering and statistics

From: De novo sequencing of sunflower genome for SNP discovery using RAD (Restriction site Associated DNA) approach

Feature

Value

Helianthus samples sequenced:

6

Total number of SNP variants identified:

105662

Total possible SNP genotypes in population:

633972

SNP genotypes with high confidence call:

502837 (79.3%)

SNP genotypes with missing or low quality data:

131135 (20.7%)

SNP loci with < 50% genotype data:

11614

SNPs passing initial filters:

94048

Number of fixed genotype calls:

448289 (89.2%)

Number of heterozygous genotype calls:

54548 (10.8%)

SNP Loci with insufficient flanking sequence for IIGT*:

3445

SNP Loci with nearby polymorphism (< 50 bp):

74136

SNP Loci meeting all defined IIGT assay design criteria:

16467

  1. * Illumina Infinium Genotyping Technology.