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 mr1311 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
vg0420718113 sf0420546156 4 20718113 2.45E-07 2.43E-07
vg0220342715 sf0220336847 2 20342715 8.87E-07 8.89E-07
vg0817557507 sf0817554793 8 17557507 8.87E-07 8.83E-07
vg0142427760 sf0142426716 1 42427760 1.23E-06 1.23E-06
vg0516508609 sf0516451091 5 16508609 1.23E-06 1.23E-06
vg0223525077 sf0223519208 2 23525077 1.81E-06 1.81E-06
vg0726559146 sf0726558152 7 26559146 1.87E-06 1.87E-06
vg0221838070 sf0221832201 2 21838070 2.27E-06 2.27E-06
vg1215307750 sf1215305048 12 15307750 2.89E-06 2.88E-06
vg1020531763 sf1020460242 10 20531763 2.95E-06 2.96E-06
vg0404029438 sf0404025045 4 4029438 3.75E-06 3.74E-06
vg0421454162 sf0421282213 4 21454162 4.66E-06 4.64E-06