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 mr1065 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
vg1209876216 sf1209873626 12 9876216 1.34E-08 1.34E-08
vg0124089174 sf0124088130 1 24089174 1.20E-07 1.20E-07
vg0311072594 sf0311071312 3 11072594 1.65E-07 1.65E-07
vg1220059260 sf1220030702 12 20059260 3.54E-07 3.54E-07
vg0614107939 sf0614106940 6 14107939 3.54E-07 3.54E-07
vg1123222536 sf1122756407 11 23222536 3.90E-07 3.90E-07
vg1222234300 sf1222200847 12 22234300 7.15E-07 7.15E-07
vg0711741544 sf0711740550 7 11741544 1.78E-06 1.78E-06
vg0118595835 sf0118594789 1 18595835 1.78E-06 1.78E-06
vg0122207812 sf0122206767 1 22207812 2.52E-06 2.52E-06
vg0900715492 sf0900714492 9 715492 3.01E-06 3.01E-06
vg0225514496 sf0225508627 2 25514496 4.16E-06 4.16E-06