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 mr1022 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
vg1215869969 sf1215867265 12 15869969 2.01E-22 1.24E-12
vg0106773680 sf0106772680 1 6773680 5.15E-11 NA
vg1213250145 sf1213247483 12 13250145 1.17E-09 NA
vg0919019906 sf0919018906 9 19019906 3.17E-09 NA
vg0812104133 sf0812103138 8 12104133 4.63E-09 NA
vg0432718715 sf0432533601 4 32718715 1.94E-07 3.87E-06
vg0433192266 sf0433007154 4 33192266 2.06E-07 5.26E-07