Additional file 1 of Beyond large-effect loci: large-scale GWAS reveals a mixed large-effect and polygenic architecture for age at maturity of Atlantic salmon
Additional file 1: Table S1. Mean discordance between imputed and actual genotypes per chromosome. Table S2. List of the 120 candidate genes tagged by the 116 significant SNPs identified with conditional and joint analysis. The P-value indicates significance of the association test performed in BOLT...
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ftdatacite:10.6084/m9.figshare.11846790 2023-05-15T15:32:38+02:00 Additional file 1 of Beyond large-effect loci: large-scale GWAS reveals a mixed large-effect and polygenic architecture for age at maturity of Atlantic salmon Sinclair-Waters, Marion Ødegård, Jørgen Korsvoll, Sven Moen, Thomas Lien, Sigbjørn Primmer, Craig Barson, Nicola 2020 https://dx.doi.org/10.6084/m9.figshare.11846790 https://springernature.figshare.com/articles/Additional_file_1_of_Beyond_large-effect_loci_large-scale_GWAS_reveals_a_mixed_large-effect_and_polygenic_architecture_for_age_at_maturity_of_Atlantic_salmon/11846790 unknown figshare https://dx.doi.org/10.1186/s12711-020-0529-8 Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode cc-by-4.0 CC-BY Genetics FOS Biological sciences Pharmacology Ecology 69999 Biological Sciences not elsewhere classified Plant Biology dataset Dataset 2020 ftdatacite https://doi.org/10.6084/m9.figshare.11846790 https://doi.org/10.1186/s12711-020-0529-8 2021-11-05T12:55:41Z Additional file 1: Table S1. Mean discordance between imputed and actual genotypes per chromosome. Table S2. List of the 120 candidate genes tagged by the 116 significant SNPs identified with conditional and joint analysis. The P-value indicates significance of the association test performed in BOLT-LMM using a non-infinitesimal model. P-value (COJO) indicates the significance of the SNP after conditional and joint analysis. Beta and its corresponding standard error (Beta_SE) were estimated using BOLT-LMM and indicate the effect size of the minor allele. The odds ratio (OR) and its corresponding transformed standard error (SE_T) were calculated using LMOR. Table S3. List of all 512,397 SNPs in the final dataset. Output statistics from BOLT-LMM (p-value, Beta & Beta_SE) and LMOR (OR, log(OR) & SE_T) are listed. The p-value indicates significance of the association test performed in BOLT-LMM using a non-infinitesimal model. Beta and its corresponding standard error (Beta_SE) were estimated using BOLT-LMM and indicate the effect size of the minor allele. The odds ratio (OR) and its corresponding transformed standard error (SE_T) were calculated using LMOR. Table S4. Estimated heritabilities from GCTA using the 50K array dataset. Estimates are given on the observed quantitative scale and when transformed on the liability scale assuming population prevalences of 1%, 2.5% and 5%. Dataset Atlantic salmon DataCite Metadata Store (German National Library of Science and Technology) |
institution |
Open Polar |
collection |
DataCite Metadata Store (German National Library of Science and Technology) |
op_collection_id |
ftdatacite |
language |
unknown |
topic |
Genetics FOS Biological sciences Pharmacology Ecology 69999 Biological Sciences not elsewhere classified Plant Biology |
spellingShingle |
Genetics FOS Biological sciences Pharmacology Ecology 69999 Biological Sciences not elsewhere classified Plant Biology Sinclair-Waters, Marion Ødegård, Jørgen Korsvoll, Sven Moen, Thomas Lien, Sigbjørn Primmer, Craig Barson, Nicola Additional file 1 of Beyond large-effect loci: large-scale GWAS reveals a mixed large-effect and polygenic architecture for age at maturity of Atlantic salmon |
topic_facet |
Genetics FOS Biological sciences Pharmacology Ecology 69999 Biological Sciences not elsewhere classified Plant Biology |
description |
Additional file 1: Table S1. Mean discordance between imputed and actual genotypes per chromosome. Table S2. List of the 120 candidate genes tagged by the 116 significant SNPs identified with conditional and joint analysis. The P-value indicates significance of the association test performed in BOLT-LMM using a non-infinitesimal model. P-value (COJO) indicates the significance of the SNP after conditional and joint analysis. Beta and its corresponding standard error (Beta_SE) were estimated using BOLT-LMM and indicate the effect size of the minor allele. The odds ratio (OR) and its corresponding transformed standard error (SE_T) were calculated using LMOR. Table S3. List of all 512,397 SNPs in the final dataset. Output statistics from BOLT-LMM (p-value, Beta & Beta_SE) and LMOR (OR, log(OR) & SE_T) are listed. The p-value indicates significance of the association test performed in BOLT-LMM using a non-infinitesimal model. Beta and its corresponding standard error (Beta_SE) were estimated using BOLT-LMM and indicate the effect size of the minor allele. The odds ratio (OR) and its corresponding transformed standard error (SE_T) were calculated using LMOR. Table S4. Estimated heritabilities from GCTA using the 50K array dataset. Estimates are given on the observed quantitative scale and when transformed on the liability scale assuming population prevalences of 1%, 2.5% and 5%. |
format |
Dataset |
author |
Sinclair-Waters, Marion Ødegård, Jørgen Korsvoll, Sven Moen, Thomas Lien, Sigbjørn Primmer, Craig Barson, Nicola |
author_facet |
Sinclair-Waters, Marion Ødegård, Jørgen Korsvoll, Sven Moen, Thomas Lien, Sigbjørn Primmer, Craig Barson, Nicola |
author_sort |
Sinclair-Waters, Marion |
title |
Additional file 1 of Beyond large-effect loci: large-scale GWAS reveals a mixed large-effect and polygenic architecture for age at maturity of Atlantic salmon |
title_short |
Additional file 1 of Beyond large-effect loci: large-scale GWAS reveals a mixed large-effect and polygenic architecture for age at maturity of Atlantic salmon |
title_full |
Additional file 1 of Beyond large-effect loci: large-scale GWAS reveals a mixed large-effect and polygenic architecture for age at maturity of Atlantic salmon |
title_fullStr |
Additional file 1 of Beyond large-effect loci: large-scale GWAS reveals a mixed large-effect and polygenic architecture for age at maturity of Atlantic salmon |
title_full_unstemmed |
Additional file 1 of Beyond large-effect loci: large-scale GWAS reveals a mixed large-effect and polygenic architecture for age at maturity of Atlantic salmon |
title_sort |
additional file 1 of beyond large-effect loci: large-scale gwas reveals a mixed large-effect and polygenic architecture for age at maturity of atlantic salmon |
publisher |
figshare |
publishDate |
2020 |
url |
https://dx.doi.org/10.6084/m9.figshare.11846790 https://springernature.figshare.com/articles/Additional_file_1_of_Beyond_large-effect_loci_large-scale_GWAS_reveals_a_mixed_large-effect_and_polygenic_architecture_for_age_at_maturity_of_Atlantic_salmon/11846790 |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_relation |
https://dx.doi.org/10.1186/s12711-020-0529-8 |
op_rights |
Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode cc-by-4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.6084/m9.figshare.11846790 https://doi.org/10.1186/s12711-020-0529-8 |
_version_ |
1766363133640704000 |