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 mr1510 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
vg0721351480 sf0721350487 7 21351480 2.71E-13 NA
vg0313992746 sf0313991463 3 13992746 1.38E-12 NA
vg0623601527 sf0623600530 6 23601527 2.38E-12 NA
vg0608245933 sf0608244934 6 8245933 3.04E-12 NA
vg0703803351 sf0703802352 7 3803351 3.34E-12 NA
vg0721364910 sf0721363917 7 21364910 7.69E-12 3.06E-06
vg0721444548 sf0721443555 7 21444548 1.16E-09 1.63E-06
vg0500152728 sf0500152728 5 152728 8.30E-09 7.20E-06
vg0726300919 sf0726299925 7 26300919 NA 4.05E-07
vg0306613252 sf0306612252 3 6613252 NA 1.34E-06
vg0709674724 sf0709673730 7 9674724 NA 4.60E-06