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 mr1197 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
vg0610060876 sf0610059877 6 10060876 1.75E-10 1.05E-07
vg0507615092 sf0507615033 5 7615092 3.65E-07 1.31E-06
vg0609809022 sf0609808023 6 9809022 4.75E-07 3.85E-06
vg0323548805 sf0323546979 3 23548805 5.07E-06 4.37E-06
vg0409762845 sf0409753543 4 9762845 NA 9.93E-07