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 mr1733 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
vg0502574829 sf0502574805 5 2574829 2.27E-11 NA
vg0709987989 sf0709986995 7 9987989 3.41E-10 NA
vg0108957658 sf0108956658 1 8957658 9.30E-10 NA
vg0720024015 sf0720023022 7 20024015 1.15E-09 NA
vg0414221572 sf0414212285 4 14221572 2.51E-09 NA
vg1003830395 sf1003829371 10 3830395 3.44E-09 NA
vg0403586262 sf0403581862 4 3586262 2.40E-08 NA
vg0917115951 sf0917114950 9 17115951 NA 5.90E-06