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 mr1746 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
vg0800341637 sf0800340637 8 341637 1.42E-14 2.74E-09
vg0812036270 sf0812035275 8 12036270 7.75E-12 NA
vg0106354885 sf0106353885 1 6354885 1.95E-11 NA
vg1119906028 sf1119439951 11 19906028 2.76E-11 NA
vg0418072521 sf0417900562 4 18072521 6.95E-11 NA
vg0622533129 sf0622532132 6 22533129 3.60E-08 NA
vg0206119753 sf0206119753 2 6119753 NA 3.12E-06