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 mr1368 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
vg1019736146 sf1019664646 10 19736146 2.50E-39 4.16E-06
vg1216532173 sf1216529466 12 16532173 3.30E-39 7.42E-06
vg1019765278 sf1019693778 10 19765278 8.64E-39 3.43E-06
vg0310319070 sf0310317986 3 10319070 4.04E-38 NA
vg0204690298 sf0204690295 2 4690298 5.74E-38 NA
vg0815857687 sf0815854973 8 15857687 1.68E-37 NA
vg1020221107 sf1020149587 10 20221107 1.17E-32 NA
vg0413765723 sf0413756437 4 13765723 NA 1.21E-07
vg0727548424 sf0727547430 7 27548424 NA 8.40E-07
vg0314211546 sf0314210235 3 14211546 NA 1.36E-06
vg1206477744 sf1206476634 12 6477744 NA 3.20E-06
vg0727531115 sf0727530121 7 27531115 NA 3.95E-06
vg0805485086 sf0805484089 8 5485086 NA 7.22E-06