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 mr1558 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
vg1209700334 sf1209697743 12 9700334 2.30E-09 5.75E-06
vg0622854546 sf0622853549 6 22854546 9.74E-06 NA
vg0235128728 sf0235122859 2 35128728 NA 2.83E-07
vg0819408037 sf0819405324 8 19408037 NA 3.75E-07
vg0235126397 sf0235120528 2 35126397 NA 5.29E-07
vg0212842545 sf0212842541 2 12842545 NA 3.72E-06
vg1209592277 sf1209589686 12 9592277 NA 4.30E-06
vg0622958104 sf0622957107 6 22958104 NA 7.70E-06