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 mr1540 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
vg1218416620 sf1218388056 12 18416620 8.41E-12 1.57E-06
vg0140642543 sf0140641500 1 40642543 2.51E-11 NA
vg0429773519 sf0429588388 4 29773519 1.00E-10 NA
vg0614652165 sf0614651166 6 14652165 1.26E-10 NA
vg1122863147 sf1122397018 11 22863147 1.56E-10 NA
vg1208123893 sf1208121299 12 8123893 3.51E-10 5.24E-07
vg1218417268 sf1218388704 12 18417268 7.10E-10 2.25E-06
vg0322274602 sf0322273109 3 22274602 3.59E-08 NA
vg0918838703 sf0918837703 9 18838703 4.97E-08 4.46E-06
vg0419756923 sf0419584958 4 19756923 7.34E-08 NA
vg0335688200 sf0335681069 3 35688200 5.20E-07 NA
vg0623114792 sf0623113795 6 23114792 NA 3.44E-06