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 mr1938 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
vg0526243037 sf0526180401 5 26243037 1.30E-17 1.42E-06
vg0525982490 sf0525919910 5 25982490 3.03E-17 1.61E-07
vg0520620361 sf0520557802 5 20620361 1.70E-15 NA
vg0614984993 sf0614983994 6 14984993 2.09E-15 NA
vg0815133905 sf0815131191 8 15133905 3.03E-15 7.37E-06
vg0503041446 sf0503041422 5 3041446 8.75E-15 NA
vg0815403093 sf0815400379 8 15403093 5.23E-12 NA
vg0406864232 sf0406859677 4 6864232 2.23E-11 NA
vg1123192315 sf1122726186 11 23192315 NA 1.36E-06