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 mr1284 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
vg0402104951 sf0402100545 4 2104951 1.17E-08 1.63E-06
vg0332498725 sf0332491598 3 32498725 4.29E-08 NA
vg0529106995 sf0529044350 5 29106995 3.20E-07 2.83E-06
vg0224820671 sf0224814802 2 24820671 3.12E-06 4.50E-06
vg1218164873 sf1218136309 12 18164873 8.20E-06 NA
vg1214093168 sf1214090508 12 14093168 NA 3.21E-07