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 mr1077 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
vg0122155873 sf0122154828 1 22155873 1.20E-09 9.13E-06
vg0135555900 sf0135554857 1 35555900 4.07E-09 NA
vg0815769876 sf0815767162 8 15769876 5.45E-09 NA
vg0314971258 sf0314969905 3 14971258 6.36E-09 6.62E-06
vg0425054754 sf0424869615 4 25054754 7.64E-09 NA
vg0604659253 sf0604658254 6 4659253 1.28E-07 1.73E-06