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 mr1578 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
vg0728454407 sf0728453415 7 28454407 5.99E-15 NA
vg0430805338 sf0430620215 4 30805338 1.40E-14 NA
vg0133316697 sf0133315653 1 33316697 1.58E-14 NA
vg0212622536 sf0212622532 2 12622536 4.11E-14 2.24E-06
vg0506131927 sf0506131866 5 6131927 6.47E-14 NA
vg0129914110 sf0129913065 1 29914110 2.76E-13 5.33E-06
vg0711021713 sf0711020719 7 11021713 2.22E-11 2.03E-06
vg1122514350 sf1122048221 11 22514350 1.21E-09 2.15E-06
vg0715840651 sf0715839658 7 15840651 3.11E-09 NA
vg1017103757 sf1017032529 10 17103757 NA 1.64E-06