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 mr1537 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
vg0211205571 sf0211205568 2 11205571 3.47E-14 NA
vg0428135712 sf0427950576 4 28135712 1.15E-13 NA
vg0420198457 sf0420026499 4 20198457 1.40E-13 NA
vg1017936465 sf1017865237 10 17936465 2.17E-13 NA
vg0124506200 sf0124505156 1 24506200 2.36E-13 NA
vg0815304114 sf0815301400 8 15304114 NA 1.40E-06
vg1120477715 sf1120011640 11 20477715 NA 7.49E-06