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 mr1696 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
vg0130213194 sf0130212149 1 30213194 1.86E-10 8.01E-06
vg1104990849 sf1104986660 11 4990849 3.72E-10 3.92E-06
vg0207854825 sf0207854824 2 7854825 6.13E-10 1.07E-06
vg0125460621 sf0125459577 1 25460621 1.88E-09 NA
vg0128534117 sf0128533072 1 28534117 2.76E-08 NA
vg1015779989 sf1015708759 10 15779989 6.39E-08 3.97E-06
vg0431411704 sf0431226602 4 31411704 7.98E-08 4.94E-06
vg1215178307 sf1215175643 12 15178307 1.05E-06 NA
vg1115880965 sf1115415835 11 15880965 3.13E-06 NA
vg1105269119 sf1105264870 11 5269119 7.67E-06 NA