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 mr1904 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
vg1102329689 sf1102325548 11 2329689 1.27E-16 2.02E-10
vg0107213426 sf0107212426 1 7213426 7.48E-12 2.90E-07
vg0417876837 sf0417704879 4 17876837 1.73E-10 NA
vg1105606704 sf1105602456 11 5606704 3.31E-10 NA
vg1218173208 sf1218144644 12 18173208 3.73E-10 NA
vg0515921851 sf0515864358 5 15921851 1.59E-09 6.49E-07
vg0412453374 sf0412444089 4 12453374 2.99E-09 5.26E-07
vg0714702171 sf0714701178 7 14702171 5.10E-07 8.02E-07
vg1001638642 sf1001637619 10 1638642 1.04E-06 4.99E-08
vg0812614023 sf0812611848 8 12614023 1.40E-06 2.58E-06
vg0806495774 sf0806494779 8 6495774 1.82E-06 NA
vg0114145813 sf0114144787 1 14145813 3.64E-06 NA