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 mr1019 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
vg1215988583 sf1215985879 12 15988583 1.13E-32 4.03E-19
vg1212877317 sf1212874656 12 12877317 1.65E-15 2.59E-06
vg0228430651 sf0228424782 2 28430651 7.07E-14 NA
vg0630798684 sf0630797686 6 30798684 1.99E-13 NA
vg1202865605 sf1202864607 12 2865605 2.41E-13 NA
vg1116068177 sf1115603049 11 16068177 2.42E-13 2.36E-06
vg1218663003 sf1218634438 12 18663003 5.71E-11 2.79E-07
vg1216138955 sf1216136251 12 16138955 NA 3.78E-09
vg1022588644 sf1022517118 10 22588644 NA 7.56E-07
vg0408293903 sf0408289177 4 8293903 NA 1.69E-06