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 mr1446 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
vg0704768024 sf0704767025 7 4768024 8.86E-08 NA
vg1123041283 sf1122575154 11 23041283 1.15E-07 1.84E-06
vg0909930571 sf0909929570 9 9930571 1.19E-06 NA
vg0212064522 sf0212064518 2 12064522 1.41E-06 2.92E-08
vg0138058961 sf0138057918 1 38058961 NA 2.17E-06
vg0133776229 sf0133775185 1 33776229 NA 3.73E-06