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 mr1778 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
vg0137255998 sf0137254955 1 37255998 1.31E-07 1.31E-07
vg0900167697 sf0900166697 9 167697 2.82E-07 2.82E-07
vg1204356347 sf1204355335 12 4356347 3.71E-07 3.71E-07
vg1217503845 sf1217497800 12 17503845 4.07E-07 4.07E-07
vg1108497933 sf1108492543 11 8497933 4.48E-07 4.48E-07
vg0122647957 sf0122646912 1 22647957 4.63E-07 4.63E-07
vg1114153307 sf1113689628 11 14153307 1.04E-06 1.04E-06
vg0230033957 sf0230028088 2 30033957 1.72E-06 1.72E-06
vg0707252342 sf0707251347 7 7252342 1.79E-06 1.79E-06
vg0408202291 sf0408197565 4 8202291 2.17E-06 2.17E-06
vg1217372943 sf1217366898 12 17372943 2.94E-06 2.94E-06
vg0324116659 sf0324114738 3 24116659 3.10E-06 3.10E-06
vg0910687363 sf0910686362 9 10687363 4.01E-06 4.01E-06
vg0318172880 sf0318171662 3 18172880 4.64E-06 4.64E-06