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 mr1980 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
vg1013583745 sf1013512515 10 13583745 9.09E-14 2.82E-08
vg0625030338 sf0625029341 6 25030338 1.81E-09 NA
vg0610932391 sf0610931392 6 10932391 2.35E-09 NA
vg0608756076 sf0608755077 6 8756076 4.56E-09 NA
vg0204032926 sf0204032923 2 4032926 5.15E-09 NA
vg0206119753 sf0206119753 2 6119753 1.79E-08 4.17E-06