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 mr1313 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
vg1218594158 sf1218565594 12 18594158 3.52E-07 3.51E-07
vg0334841623 sf0334834493 3 34841623 6.89E-07 6.90E-07
vg0600024617 sf0600023617 6 24617 9.59E-07 9.59E-07
vg0701185368 sf0701184368 7 1185368 1.09E-06 1.09E-06
vg0306112685 sf0306111685 3 6112685 1.48E-06 1.48E-06
vg0211103497 sf0211103494 2 11103497 4.19E-06 4.20E-06
vg1020503467 sf1020431946 10 20503467 4.53E-06 4.54E-06
vg0715470958 sf0715469965 7 15470958 4.76E-06 4.76E-06