Citation: T. Schmutzer (2015-05-22): Brassica_napus_SNPmatrix_52genotypes_PreBreed_Yield.zip. Size: 75.7 MB

Abstract: Variant calling has been performed with three different prediction methods using the tools FaSD, Freebayes and samtools. This allowed us to use the variant caller count (VCC) as an additional confidence value for the prediction of variant positions (VP). The VCC indicates how many variant calling methods predict the particular VP. All displayed VPs succeed in at least one of the genotypes the following criteria: bi-allelic, SNP quality score >= 100, homozygous, read depth >= 4 and a VCC >= 2. For each position and each genotype the putative allele(s) for the different variants are shown. For differentiation of homozygous and heterozygous positions all alternative alleles are required to succeed the minimal read depth >= 4. Genotypes with no or not sufficient read information (read depth <4) are presented as ‘NA’, positions with no alternative allele call are presented with the reference allele. A position is defined as homozygous, when the allele frequency (AF) in one of the variants is <10% or >90%. Homozygous positions are displayed by the corresponding nucleotides (‘AA’, ‘CC’, ‘GG’, ‘TT’), heterozygous positions (10% <= AF <=90%) with both observed alleles. Per genotype we only present the bi-allelic relationship using the first two major alleles.

License: CC BY 4.0 (Creative Commons Attribution)