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 mr1823 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
vg0623833223 sf0623832226 6 23833223 5.42E-09 5.42E-09
vg0919939971 sf0919939490 9 19939971 1.45E-08 1.45E-08
vg0109929600 sf0109928576 1 9929600 1.40E-06 1.40E-06
vg1000028876 sf1000027876 10 28876 3.41E-06 3.41E-06
vg0504650681 sf0504650658 5 4650681 3.80E-06 3.80E-06
vg0211790176 sf0211790172 2 11790176 4.80E-06 4.80E-06