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 mr1342 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
vg0228211458 sf0228205589 2 28211458 8.21E-13 4.69E-06
vg0622302006 sf0622301009 6 22302006 2.21E-12 NA
vg0918033763 sf0918032762 9 18033763 3.40E-12 6.03E-06
vg0719440722 sf0719439729 7 19440722 6.51E-12 NA
vg0520403770 sf0520341242 5 20403770 6.58E-12 NA
vg0224817907 sf0224812038 2 24817907 7.46E-11 NA
vg0821911860 sf0821909147 8 21911860 1.51E-10 NA
vg1223038204 sf1223004664 12 23038204 NA 6.13E-07
vg0809876655 sf0809875659 8 9876655 NA 1.38E-06
vg1002768046 sf1002767023 10 2768046 NA 4.74E-06
vg0522735034 sf0522672476 5 22735034 NA 9.19E-06