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 mr1892 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
vg1211773333 sf1211770669 12 11773333 1.86E-10 NA
vg0226834402 sf0226828533 2 26834402 8.18E-10 4.83E-06
vg0413981432 sf0413972147 4 13981432 2.97E-08 NA
vg0101639997 sf0101638997 1 1639997 4.23E-08 NA
vg0713020569 sf0713019576 7 13020569 5.07E-08 5.16E-06
vg0909146176 sf0909145175 9 9146176 2.62E-06 NA
vg0910044928 sf0910043927 9 10044928 3.25E-06 5.15E-06