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 mr1763 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
vg0726847020 sf0726846026 7 26847020 3.27E-09 2.10E-06
vg0220407461 sf0220401593 2 20407461 1.33E-08 NA
vg1104978992 sf1104974803 11 4978992 1.52E-08 NA
vg0217789129 sf0217783260 2 17789129 4.27E-08 NA
vg0125460828 sf0125459784 1 25460828 9.04E-08 NA
vg0906503065 sf0906502065 9 6503065 1.53E-07 3.49E-06
vg1106375766 sf1106371518 11 6375766 3.52E-07 8.03E-08
vg0514011016 sf0513953560 5 14011016 5.18E-07 4.72E-06
vg0219418052 sf0219412184 2 19418052 2.42E-06 NA
vg0300249514 sf0300248514 3 249514 3.94E-06 NA
vg1124078257 sf1123612127 11 24078257 5.66E-06 9.45E-07