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 mr1824 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
vg0618125425 sf0618124428 6 18125425 5.96E-11 1.30E-06
vg1122067670 sf1121601541 11 22067670 7.28E-11 6.83E-07
vg1215235888 sf1218062462 12 15235888 1.75E-10 4.52E-06
vg0910742193 sf0910741192 9 10742193 3.74E-10 9.47E-06
vg0135794714 sf0135793671 1 35794714 5.28E-10 NA
vg1122336770 sf1121870641 11 22336770 3.48E-07 3.60E-06
vg1217810691 sf1217782125 12 17810691 NA 4.37E-06
vg0713417596 sf0713416603 7 13417596 NA 4.64E-06
vg0134655954 sf0134654911 1 34655954 NA 4.87E-06