Journal: bioRxiv

Article Title: Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls

doi: 10.1101/2020.09.01.276758

Figure Lengend Snippet: Only SNPs with a significant BLAST result on the expected chromosome were considered (N=17,250).

Article Snippet: However, this trend was only observed across a small number of SNPs, as only few SNPs with many BLAST results passed the Infinium data curation step.

Techniques:

Journal: bioRxiv

Article Title: Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls

doi: 10.1101/2020.09.01.276758

Figure Lengend Snippet: Three different stringency thresholds for a successful BLAST result were used: 1E-12, 1E-14, and 1E-16. The number of SNPs within each group is listed in the included table. Higher numbers of BLAST results were grouped together because of the diminishing number of SNPs that had higher numbers of BLAST results.

Article Snippet: However, this trend was only observed across a small number of SNPs, as only few SNPs with many BLAST results passed the Infinium data curation step.

Techniques:

Journal: bioRxiv

Article Title: Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls

doi: 10.1101/2020.09.01.276758

Figure Lengend Snippet: The inclusion rate of Infinium data is represented by black and the compatibility of these included SNPs with Axiom data with and without class C SNPs (those with additional heterozygous cluster(s) in Axiom cluster plots requiring manual adjustment to make compatible) being classified as compatible are represented by pink and blue, respectively. The horizontal lines represent the inclusion and compatibility rates for SNPs with no identified secondary polymorphisms at their probe site for the three respective data sources that sized 6,632 (black), 6,011 (pink), and 6,011 (blue) SNPs. SNPs included in this analysis had their alternate allele present in at least 10% of the sequenced individuals, had no more than 25% missing data across the sequenced individuals, and had probe sequence with a single BLAST result on the GDDH13 WGS with an E-value <1E-12.

Article Snippet: However, this trend was only observed across a small number of SNPs, as only few SNPs with many BLAST results passed the Infinium data curation step.

Techniques: Sequencing