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 mr1940 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
vg1206159410 sf1206158301 12 6159410 5.96E-08 1.51E-07
vg1206877221 sf1206876111 12 6877221 2.72E-07 7.03E-07
vg0727965800 sf0727964807 7 27965800 4.59E-07 6.22E-07
vg0504217889 sf0504217866 5 4217889 1.27E-06 NA
vg0819138103 sf0819135390 8 19138103 1.40E-06 NA
vg1206195784 sf1206194675 12 6195784 1.48E-06 7.07E-07