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 mr1844 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
vg1016937932 sf1016866704 10 16937932 7.90E-17 NA
vg0311342165 sf0311340883 3 11342165 3.49E-16 8.13E-06
vg0815698752 sf0815696038 8 15698752 5.77E-16 NA
vg0132085326 sf0132084282 1 32085326 6.57E-16 NA
vg0122975023 sf0122973979 1 22975023 8.64E-16 NA
vg0716058721 sf0716057728 7 16058721 NA 1.80E-07
vg0629374171 sf0629373173 6 29374171 NA 1.24E-06
vg0412756324 sf0412747034 4 12756324 NA 2.88E-06
vg1011517194 sf1011446013 10 11517194 NA 5.87E-06