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 mr1939 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
vg0820974361 sf0820971648 8 20974361 2.60E-06 2.60E-06
vg0719981901 sf0719980908 7 19981901 3.26E-06 3.26E-06
vg1107375253 sf1107370998 11 7375253 4.15E-06 4.14E-06
vg0131880868 sf0131879824 1 31880868 4.34E-06 4.34E-06
vg1125773021 sf1125306860 11 25773021 4.54E-06 4.54E-06
vg1007900043 sf1007915653 10 7900043 4.64E-06 4.64E-06