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 mr1520 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
vg0408266266 sf0408261540 4 8266266 8.02E-16 NA
vg0129977730 sf0129976685 1 29977730 1.86E-15 3.78E-06
vg0129982794 sf0129981749 1 29982794 2.26E-15 2.97E-06
vg0411081023 sf0411071724 4 11081023 5.70E-15 NA
vg0306322887 sf0306321887 3 6322887 1.05E-14 NA
vg0516238432 sf0516180914 5 16238432 1.02E-13 NA
vg0922495667 sf0922495186 9 22495667 NA 1.84E-06
vg0819104472 sf0819101759 8 19104472 NA 4.47E-06
vg1128159591 sf1127636370 11 28159591 NA 6.60E-06