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 mr1932 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
vg0528196605 sf0528133960 5 28196605 1.65E-07 2.66E-08
vg0824162398 sf0824159684 8 24162398 1.18E-06 2.18E-06
vg0336367247 sf0336360117 3 36367247 1.95E-06 2.14E-06
vg0610602877 sf0610601878 6 10602877 NA 1.56E-06
vg0528917046 sf0528854401 5 28917046 NA 3.00E-06
vg1015877393 sf1015806163 10 15877393 NA 3.13E-06