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Concordance rate in cattle and sheep between genotypes differing in Illumina GenCall quality score
- Source :
- Animal geneticsReferences. 52(2)
- Publication Year :
- 2021
-
Abstract
- Proper quality control of data prior to downstream analyses is fundamental to ensure integrity of results; quality control of genomic data is no exception. While many metrics of quality control of genomic data exist, the objective of the present study was to quantify the genotype and allele concordance rate between called single nucleotide polymorphism (SNP) genotypes differing in GenCall (GC) score; the GC score is a confidence measure assigned to each Illumina genotype call. This objective was achieved using Illumina beadchip genotype data from 771 cattle (12 428 767 genotypes in total post-editing) and 80 sheep (1 557 360 SNPs genotypes in total post-editing) each genotyped in duplicate. The called genotype with the lowest associated GC score was compared to the genotype called for the same SNP in the same duplicated animal sample but with a GC score of >0.90 (assumed to represent the true genotype). The mean genotype concordance rate for a GC score of
- Subjects :
- 0301 basic medicine
Genotype
Concordance
Genomic data
Population
Single-nucleotide polymorphism
Biology
Polymorphism, Single Nucleotide
03 medical and health sciences
Genetics
SNP
Animals
Allele
education
Alleles
education.field_of_study
Sheep
0402 animal and dairy science
High-Throughput Nucleotide Sequencing
04 agricultural and veterinary sciences
General Medicine
Genomics
040201 dairy & animal science
030104 developmental biology
Quality Score
Animal Science and Zoology
Cattle
Subjects
Details
- ISSN :
- 13652052
- Volume :
- 52
- Issue :
- 2
- Database :
- OpenAIRE
- Journal :
- Animal geneticsReferences
- Accession number :
- edsair.doi.dedup.....ae4f4db328b6d053646bb94feeab231c