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 mr1578 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
vg1214578422 sf1214575762 12 14578422 6.01E-09 2.17E-06
vg1214655843 sf1214653183 12 14655843 6.52E-09 8.64E-06
vg0608915375 sf0608914376 6 8915375 4.71E-08 NA
vg1210414574 sf1210411987 12 10414574 7.73E-08 1.85E-06
vg0501780039 sf0501780022 5 1780039 6.90E-07 5.42E-07
vg1204380405 sf1204379393 12 4380405 8.32E-07 4.71E-07
vg0516508609 sf0516451091 5 16508609 2.65E-06 2.00E-06
vg0205968700 sf0205968700 2 5968700 4.08E-06 2.51E-07