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 mr1358 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
vg0726583506 sf0726582512 7 26583506 1.68E-09 3.21E-07
vg1221694446 sf1221660993 12 21694446 1.01E-08 3.41E-07
vg1002823994 sf1002822971 10 2823994 3.56E-08 2.22E-06
vg0304141111 sf0304140113 3 4141111 4.47E-08 NA
vg0413126535 sf0413117245 4 13126535 6.72E-08 5.89E-06
vg1003749596 sf1003748573 10 3749596 1.36E-07 2.89E-06
vg0205570340 sf0205570340 2 5570340 3.64E-07 9.90E-06
vg0818818092 sf0818815379 8 18818092 2.24E-06 2.61E-07