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 mr1521 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
vg1209239750 sf1209237159 12 9239750 8.76E-08 1.93E-06
vg1022385882 sf1022314356 10 22385882 8.92E-08 NA
vg1020006876 sf1019935375 10 20006876 4.39E-07 1.87E-07
vg0418940275 sf0418768320 4 18940275 4.99E-07 3.77E-07
vg0327524627 sf0327517680 3 27524627 1.89E-06 2.44E-06
vg1006489415 sf1006505038 10 6489415 2.73E-06 1.66E-06
vg0418759478 sf0418587523 4 18759478 4.08E-06 3.74E-07
vg1106375766 sf1106371518 11 6375766 9.92E-06 3.01E-06