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 mr1729 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
vg1117477253 sf1117011108 11 17477253 1.93E-11 5.39E-07
vg1117178010 sf1116711862 11 17178010 2.70E-09 NA
vg1119258661 sf1118792349 11 19258661 4.37E-09 NA
vg1200558750 sf1200557750 12 558750 1.88E-08 NA
vg0431520593 sf0431335492 4 31520593 1.95E-08 NA
vg0328933796 sf0328926848 3 28933796 3.35E-08 3.84E-06
vg1200292611 sf1200291611 12 292611 2.75E-07 NA
vg0113677789 sf0113676763 1 13677789 NA 4.76E-06