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 mr1897 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
vg0216758815 sf0216752945 2 16758815 7.78E-14 4.02E-11
vg0217023878 sf0217018008 2 17023878 7.86E-14 2.90E-11
vg0205409502 sf0205409502 2 5409502 2.86E-08 NA
vg0729360051 sf0729359059 7 29360051 1.45E-07 2.53E-06
vg0205197111 sf0205197108 2 5197111 1.33E-06 1.27E-06
vg0509750750 sf0509750679 5 9750750 4.23E-06 NA