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 mr1164 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
vg0623833223 sf0623832226 6 23833223 1.62E-08 1.62E-08
vg1011021357 sf1010950177 10 11021357 3.95E-08 3.95E-08
vg1127372010 sf1126900397 11 27372010 9.27E-07 9.27E-07
vg1116350295 sf1115885171 11 16350295 1.05E-06 1.05E-06
vg1122668782 sf1122202653 11 22668782 1.87E-06 1.87E-06
vg0217796101 sf0217790232 2 17796101 3.30E-06 3.30E-06