Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1534 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0626212882 sf0626211885 6 26212882 2.48E-11 7.55E-07
vg0626188532 sf0626187535 6 26188532 1.36E-10 1.01E-06
vg0622302006 sf0622301009 6 22302006 4.82E-10 6.32E-07
vg0113550043 sf0113549017 1 13550043 2.44E-09 NA
vg1117116576 sf1116650428 11 17116576 4.30E-09 NA
vg1200618450 sf1200617450 12 618450 1.79E-08 NA
vg0617811733 sf0617810736 6 17811733 6.16E-08 4.39E-06
vg0626719833 sf0626718836 6 26719833 6.93E-08 2.40E-07
vg0606864427 sf0606863428 6 6864427 7.57E-08 NA
vg0622510881 sf0622509884 6 22510881 3.56E-07 NA