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 mr1270 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
vg0521875329 sf0521812771 5 21875329 6.62E-08 5.47E-08
vg0226712993 sf0226707124 2 26712993 1.63E-07 1.90E-06
vg0707463836 sf0707462841 7 7463836 1.98E-07 2.07E-06
vg0528196605 sf0528133960 5 28196605 8.02E-07 3.22E-06
vg1213234552 sf1213231890 12 13234552 3.72E-06 NA
vg0514011016 sf0513953560 5 14011016 NA 4.01E-06