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 mr1030 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
vg0424056995 sf0423871856 4 24056995 9.36E-09 2.86E-06
vg1218169210 sf1218140646 12 18169210 1.17E-08 1.05E-06
vg0424042945 sf0423857805 4 24042945 1.28E-08 1.96E-06
vg1218169215 sf1218140651 12 18169215 9.16E-08 5.28E-07
vg1221892295 sf1221858842 12 21892295 2.82E-06 NA
vg0507693857 sf0507693798 5 7693857 NA 7.41E-06