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 mr1387 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
vg0708445190 sf0708444195 7 8445190 1.92E-06 1.92E-06
vg0224869035 sf0224863166 2 24869035 2.63E-06 2.63E-06
vg1216729892 sf1216723846 12 16729892 3.28E-06 3.28E-06
vg0219809349 sf0219803481 2 19809349 4.71E-06 4.71E-06
vg0816203674 sf0816200960 8 16203674 4.76E-06 4.76E-06
vg0216120581 sf0216114711 2 16120581 7.09E-06 7.09E-06
vg0620348476 sf0620347479 6 20348476 9.33E-06 9.33E-06