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 mr1784 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
vg1018583477 sf1018512034 10 18583477 8.71E-20 1.82E-07
vg0523062907 sf0523000348 5 23062907 4.01E-15 NA
vg0515563729 sf0515506270 5 15563729 5.49E-15 NA
vg0503985420 sf0503985397 5 3985420 1.80E-14 NA
vg1010518357 sf1010447178 10 10518357 5.90E-14 NA
vg0619939165 sf0619938168 6 19939165 NA 1.62E-06
vg0819246479 sf0819243766 8 19246479 NA 5.20E-06