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 mr1851 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
vg0419219689 sf0419047727 4 19219689 1.85E-40 2.74E-31
vg0419216517 sf0419044555 4 19216517 2.02E-40 2.50E-31
vg0810571030 sf0810570034 8 10571030 1.46E-11 NA
vg0419205007 sf0419033043 4 19205007 9.61E-11 1.96E-09
vg0813845332 sf0813842618 8 13845332 2.32E-10 NA
vg0418870189 sf0418698234 4 18870189 2.84E-10 3.73E-06
vg0418868784 sf0418696829 4 18868784 6.18E-10 6.84E-07
vg0419225881 sf0419053919 4 19225881 2.01E-07 1.02E-11
vg0629542107 sf0629541109 6 29542107 6.73E-07 3.96E-06
vg0620348476 sf0620347479 6 20348476 1.42E-06 5.55E-07
vg0804861961 sf0804860964 8 4861961 NA 8.04E-07
vg1222398998 sf1222365437 12 22398998 NA 4.33E-06