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 mr1889 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
vg0524718407 sf0524655827 5 24718407 1.43E-33 2.14E-15
vg0524598675 sf0524536095 5 24598675 7.96E-33 8.21E-16
vg1100250151 sf1100249153 11 250151 2.47E-22 2.61E-09
vg1100016479 sf1100015479 11 16479 3.50E-15 2.05E-07
vg0524331456 sf0524268875 5 24331456 5.55E-15 5.01E-06
vg1200003632 sf1200002632 12 3632 5.57E-15 NA
vg0433393939 sf0433208828 4 33393939 3.84E-13 7.70E-06
vg0605931332 sf0605930333 6 5931332 3.42E-09 1.62E-06
vg0431941468 sf0431756363 4 31941468 4.68E-09 NA
vg1208947655 sf1208945063 12 8947655 2.59E-08 9.24E-07
vg1217385743 sf1217379698 12 17385743 NA 2.83E-06
vg1207815198 sf1207812604 12 7815198 NA 4.91E-06