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 mr1369 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
vg1216110511 sf1216107807 12 16110511 3.75E-11 2.69E-08
vg0727110534 sf0727109540 7 27110534 4.00E-11 7.68E-07
vg0727171704 sf0727170710 7 27171704 1.02E-10 5.46E-07
vg0129095966 sf0129094921 1 29095966 1.98E-10 2.25E-06
vg1020531763 sf1020460242 10 20531763 3.43E-10 2.01E-06
vg0801629021 sf0801628023 8 1629021 3.61E-10 NA
vg0207665511 sf0207665511 2 7665511 5.15E-09 2.77E-06
vg0716434420 sf0716433427 7 16434420 4.22E-07 2.08E-06
vg0124440740 sf0124439696 1 24440740 NA 3.64E-06
vg0124420497 sf0124419453 1 24420497 NA 4.83E-06
vg0312184618 sf0312183336 3 12184618 NA 4.97E-06