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 mr1748 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
vg0823006156 sf0823003443 8 23006156 1.15E-09 1.16E-06
vg0703878959 sf0703877960 7 3878959 1.69E-08 NA
vg0524300403 sf0524237822 5 24300403 1.76E-08 NA
vg0617992086 sf0617991089 6 17992086 4.04E-08 NA
vg0405776502 sf0405771941 4 5776502 8.28E-06 NA
vg0828199395 sf0828196681 8 28199395 9.02E-06 NA
vg1217693047 sf1217687002 12 17693047 NA 4.75E-06