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 mr1780 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
vg1210134367 sf1210131778 12 10134367 1.22E-40 NA
vg0217207426 sf0217201556 2 17207426 1.33E-39 NA
vg0807319112 sf0807318117 8 7319112 2.57E-39 NA
vg1215975817 sf1215973113 12 15975817 1.24E-38 NA
vg0206250874 sf0206250874 2 6250874 1.24E-36 NA
vg0807179141 sf0807178146 8 7179141 3.19E-36 NA
vg1017942904 sf1017871676 10 17942904 7.22E-33 NA
vg1210574208 sf1210571621 12 10574208 1.74E-32 8.13E-07
vg0400137046 sf0400136046 4 137046 2.26E-32 3.11E-07