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 mr1229 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
vg1016820823 sf1016749595 10 16820823 1.80E-11 1.29E-06
vg0901360162 sf0901359162 9 1360162 1.94E-11 1.03E-06
vg0414346037 sf0414336750 4 14346037 1.58E-10 NA
vg0204870001 sf0204869998 2 4870001 4.03E-10 NA
vg0418575339 sf0418403384 4 18575339 5.32E-10 NA
vg1103859312 sf1103855214 11 3859312 9.71E-08 NA
vg0716392399 sf0716391406 7 16392399 2.37E-07 NA