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 mr1610 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
vg0403315819 sf0403311422 4 3315819 2.17E-08 2.17E-08
vg0202626444 sf0202626442 2 2626444 1.76E-07 1.76E-07
vg0316846972 sf0316845846 3 16846972 4.16E-07 4.16E-07
vg0121693256 sf0121692211 1 21693256 5.75E-07 5.76E-07
vg0319788098 sf0319786609 3 19788098 9.98E-07 9.99E-07
vg0430882025 sf0430696903 4 30882025 1.06E-06 1.06E-06
vg1212615976 sf1212613315 12 12615976 1.23E-06 1.23E-06
vg0917292546 sf0917291545 9 17292546 1.75E-06 1.75E-06
vg0202777372 sf0202777370 2 2777372 1.77E-06 1.77E-06
vg0217098802 sf0217092932 2 17098802 2.09E-06 2.09E-06
vg0800851933 sf0800850935 8 851933 2.29E-06 2.29E-06
vg0119110815 sf0119109770 1 19110815 2.67E-06 2.67E-06
vg1013566081 sf1013494851 10 13566081 3.23E-06 3.23E-06
vg1100364259 sf1100363261 11 364259 3.69E-06 3.69E-06
vg0419947958 sf0419775994 4 19947958 3.99E-06 3.99E-06
vg0505090444 sf0524866233 5 5090444 4.02E-06 4.02E-06