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 mr1575 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
vg0104592748 sf0104591748 1 4592748 4.42E-13 3.45E-07
vg1218087228 sf1218058664 12 18087228 5.78E-12 8.15E-06
vg0528402446 sf0528339801 5 28402446 1.01E-11 2.06E-06
vg0315094287 sf0315092934 3 15094287 1.56E-11 NA
vg0600664678 sf0600663679 6 664678 2.72E-11 NA
vg1226390556 sf1226356950 12 26390556 2.68E-10 4.19E-06