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 mr1902 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
vg0724515347 sf0724514353 7 24515347 2.67E-16 8.27E-14
vg1011836497 sf1011765312 10 11836497 9.99E-09 7.44E-06
vg1017092925 sf1017021697 10 17092925 1.86E-08 NA
vg1011673523 sf1011602338 10 11673523 2.03E-08 NA
vg0325099885 sf0325097966 3 25099885 7.37E-08 NA
vg0728925896 sf0728924904 7 28925896 9.86E-08 7.07E-07
vg0724473520 sf0724472526 7 24473520 NA 3.03E-08
vg0721876471 sf0721875478 7 21876471 NA 2.49E-06