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 mr1329 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
vg0420718113 sf0420546156 4 20718113 2.40E-08 2.40E-08
vg0421030366 sf0420858419 4 21030366 3.57E-08 3.57E-08
vg0424181194 sf0423996055 4 24181194 7.59E-08 7.59E-08
vg0421031577 sf0420859630 4 21031577 1.94E-07 1.94E-07
vg0516508609 sf0516451091 5 16508609 2.03E-07 2.03E-07
vg0421384856 sf0421212909 4 21384856 4.91E-07 4.91E-07
vg0704864945 sf0704863946 7 4864945 6.35E-07 6.35E-07
vg0805826839 sf0805825842 8 5826839 6.91E-07 6.91E-07
vg0607659813 sf0607658814 6 7659813 9.03E-07 9.03E-07
vg0403204105 sf0403199708 4 3204105 1.02E-06 1.02E-06
vg1124705653 sf1124239493 11 24705653 1.19E-06 1.19E-06
vg0223522667 sf0223516798 2 23522667 1.38E-06 1.38E-06
vg0909710935 sf0909709934 9 9710935 1.47E-06 1.47E-06
vg0110779745 sf0110778721 1 10779745 1.96E-06 1.96E-06
vg1225484489 sf1225450884 12 25484489 2.56E-06 2.56E-06
vg0420798136 sf0420626179 4 20798136 3.97E-06 3.97E-06
vg1108255008 sf1108249618 11 8255008 4.47E-06 4.47E-06