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 mr1471 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
vg0908755951 sf0908754950 9 8755951 2.03E-11 1.76E-07
vg0601801709 sf0601800710 6 1801709 8.41E-11 2.06E-07
vg1114456299 sf1113992616 11 14456299 2.50E-10 6.65E-07
vg1217241436 sf1217235391 12 17241436 3.03E-10 3.89E-07
vg1004557367 sf1004573905 10 4557367 4.67E-10 1.62E-06
vg0616844584 sf0616843586 6 16844584 1.05E-09 3.73E-07
vg1203994564 sf1203993552 12 3994564 1.40E-09 1.74E-06
vg1212504438 sf1212501777 12 12504438 3.63E-09 4.76E-06
vg0140061111 sf0140060068 1 40061111 1.02E-08 2.83E-06
vg0312773945 sf0312772663 3 12773945 1.27E-08 1.82E-06
vg0714324691 sf0714323698 7 14324691 1.36E-08 4.27E-06