12711_2022_732_MOESM3_ESM.pdf (45.44 kB)
Additional file 3 of Rare and population-specific functional variation across pig lines
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posted on 2022-06-04, 15:27 authored by Roger Ros-Freixedes, Bruno D. Valente, Ching-Yi Chen, William O. Herring, Gregor Gorjanc, John M. Hickey, Martin JohnssonAdditional file 3: Table S1. Number of analysed variants by chromosome.
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Biotechnology and Biological Sciences Research Council Innovate UK Svenska Forskningsrådet Formas Genus plc
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still limited knowledgeintermediate allele frequencieshigh linkage disequilibriumalternative allele frequencygenomic breeding valuessite wright ’lower allele frequenciesexplained small fractionsdifferent genetic backgroundcommercial livestock populationsparticular regarding populationnoticeably benefit acrosslow recombination rateaverage sequencing coveragepredicted functional annotationnine lines ).breed genomic predictionincluding intergenic variantsgenomic regionssmall subsetsite fstpredicted consequenceslower fstlivestock speciesgenetic linesbreed analysesincluding lofwidespread ).variant segregatedtherefore unlikelyspecific variationsignificant onessignificant lowrelated individualsregulatory variantsregulatory rolesputatively functionalproduction traitsprevalence variantsprevalence levelphenotypic variancephenotypic differencesmainly missenseimputed wholefixation indexexisting missensedistribution alongcategorized accordingassociated lowaffect applications7848 individuals610 pedigree2 %)1 ×)
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