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 mr1538 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
vg1003072838 sf1003071815 10 3072838 3.19E-16 4.11E-14
vg0137832714 sf0137831671 1 37832714 5.65E-16 1.25E-12
vg0137882391 sf0137881348 1 37882391 9.64E-15 3.98E-13
vg0137919047 sf0137918004 1 37919047 1.22E-13 7.43E-13
vg1209942861 sf1209940271 12 9942861 3.72E-11 6.93E-09
vg1016071802 sf1016000574 10 16071802 7.21E-09 9.91E-08
vg1003311148 sf1003310125 10 3311148 2.23E-08 7.42E-07
vg0126937236 sf0136872976 1 26937236 6.14E-08 3.19E-09
vg0717726887 sf0717725894 7 17726887 1.34E-07 4.60E-07
vg0422509978 sf0422324865 4 22509978 2.32E-07 2.85E-06
vg1208975006 sf1208972414 12 8975006 2.63E-07 3.88E-06
vg1003397130 sf1003396107 10 3397130 3.53E-07 4.12E-07
vg0211784188 sf0211784184 2 11784188 7.56E-07 2.72E-06
vg0317228312 sf0317227122 3 17228312 9.78E-07 1.49E-06
vg0611197637 sf0611196638 6 11197637 1.12E-06 3.18E-06
vg0421396071 sf0421224124 4 21396071 NA 2.79E-06