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 mr1216 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
vg0719199004 sf0719198011 7 19199004 6.46E-19 1.57E-10
vg0305031973 sf0305030975 3 5031973 1.78E-15 4.58E-06
vg0801160172 sf0801159174 8 1160172 2.38E-15 NA
vg0314646110 sf0314644797 3 14646110 5.44E-15 NA
vg0619806653 sf0619805656 6 19806653 3.61E-14 NA
vg0110539868 sf0110538844 1 10539868 1.81E-13 NA
vg0801511665 sf0801510667 8 1511665 1.33E-12 4.13E-07
vg1001332178 sf1001331155 10 1332178 2.91E-12 NA
vg1116788419 sf1116323297 11 16788419 7.18E-11 NA
vg0335411667 sf0335404536 3 35411667 NA 1.40E-07
vg0920039290 sf0920038809 9 20039290 NA 6.18E-07
vg0107647091 sf0107646091 1 7647091 NA 9.74E-07
vg0702247112 sf0702246113 7 2247112 NA 9.74E-07
vg0420365084 sf0420193128 4 20365084 NA 1.26E-06
vg0141203398 sf0141202355 1 41203398 NA 1.33E-06
vg0920135790 sf0920135309 9 20135790 NA 1.64E-06
vg1207840086 sf1207837492 12 7840086 NA 1.78E-06
vg0335487182 sf0335480051 3 35487182 NA 3.62E-06
vg0719091461 sf0719090468 7 19091461 NA 4.61E-06
vg0920288300 sf0920287819 9 20288300 NA 5.51E-06