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 mr1397 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
vg1020508139 sf1020436618 10 20508139 2.01E-10 3.36E-08
vg0220342715 sf0220336847 2 20342715 2.25E-09 3.63E-06
vg0132988931 sf0132987887 1 32988931 7.03E-09 NA
vg1117799956 sf1117333812 11 17799956 8.19E-09 NA
vg0142427760 sf0142426716 1 42427760 1.06E-08 9.90E-07
vg0706192930 sf0706191931 7 6192930 3.98E-08 3.74E-06
vg0808428148 sf0808427152 8 8428148 6.37E-08 8.54E-07
vg0516508609 sf0516451091 5 16508609 1.96E-06 1.24E-06
vg0626935791 sf0626934794 6 26935791 2.61E-06 1.16E-06
vg0817557507 sf0817554793 8 17557507 4.51E-06 3.41E-06
vg0513235168 sf0513178090 5 13235168 NA 1.91E-06
vg0819150140 sf0819147427 8 19150140 NA 2.45E-06
vg1215307750 sf1215305048 12 15307750 NA 7.58E-06