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 mr1856 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
vg0223518528 sf0223512659 2 23518528 1.55E-09 NA
vg0132005816 sf0132004772 1 32005816 3.04E-09 NA
vg1217569480 sf1217563435 12 17569480 6.45E-09 NA
vg1118365111 sf1117898969 11 18365111 1.47E-08 NA
vg0527921737 sf0527859094 5 27921737 1.97E-08 NA
vg0816931318 sf0816928604 8 16931318 3.11E-08 5.19E-06
vg0203000556 sf0203000554 2 3000556 7.97E-06 3.58E-06