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 mr1514 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
vg0506943490 sf0506943432 5 6943490 2.26E-13 1.70E-07
vg0506920183 sf0506920125 5 6920183 3.94E-13 2.64E-07
vg0514684611 sf0514627154 5 14684611 1.95E-12 5.71E-06
vg0327940747 sf0327933801 3 27940747 2.35E-11 NA
vg0115948322 sf0115947296 1 15948322 5.74E-11 NA
vg0310279483 sf0310278399 3 10279483 8.00E-11 NA
vg0501802982 sf0501802965 5 1802982 1.29E-10 2.10E-07
vg1001385309 sf1001384286 10 1385309 2.37E-10 4.09E-06
vg0327302530 sf0327295583 3 27302530 NA 1.28E-07
vg0518946351 sf0518883835 5 18946351 NA 2.73E-06