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 mr1482 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
vg0327912257 sf0327905311 3 27912257 3.11E-09 NA
vg1117584893 sf1117118750 11 17584893 1.26E-08 2.52E-06
vg0516758193 sf0516697835 5 16758193 2.62E-08 NA
vg1127857666 sf1127386052 11 27857666 4.60E-08 8.59E-06
vg0915924541 sf0915923540 9 15924541 4.98E-08 NA
vg0206843146 sf0206843146 2 6843146 6.90E-08 9.84E-07
vg0328193610 sf0328186664 3 28193610 6.09E-07 NA
vg0211327855 sf0211327852 2 11327855 2.85E-06 1.94E-06
vg0714389495 sf0714388502 7 14389495 6.76E-06 6.24E-06
vg1207492115 sf1207489521 12 7492115 NA 1.50E-06