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 mr1412 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
vg0805900956 sf0805899959 8 5900956 2.97E-08 2.97E-08
vg0138706549 sf0138705506 1 38706549 3.17E-07 3.17E-07
vg0804905723 sf0804904726 8 4905723 6.06E-07 6.06E-07
vg0124420479 sf0124419435 1 24420479 1.09E-06 1.09E-06
vg0222002131 sf0221996262 2 22002131 1.40E-06 1.40E-06
vg1001247868 sf1001246845 10 1247868 1.55E-06 1.55E-06
vg0317372993 sf0317371803 3 17372993 2.20E-06 2.20E-06
vg0218610196 sf0218604327 2 18610196 3.30E-06 3.31E-06
vg0324965295 sf0324963375 3 24965295 3.38E-06 3.38E-06
vg1013182968 sf1013111738 10 13182968 4.02E-06 4.02E-06
vg0207698155 sf0207698154 2 7698155 4.20E-06 4.20E-06