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 mr1316 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
vg0317961921 sf0317960703 3 17961921 1.36E-27 1.59E-06
vg0707203111 sf0707202116 7 7203111 2.95E-27 NA
vg1017965103 sf1017893875 10 17965103 7.57E-27 NA
vg1200180389 sf1200179389 12 180389 9.51E-27 8.33E-06
vg0520584620 sf0520522061 5 20584620 1.21E-25 NA
vg0213822496 sf0213816626 2 13822496 2.13E-25 3.17E-06
vg1200181061 sf1200180061 12 181061 4.12E-25 NA
vg0510324989 sf0510324918 5 10324989 NA 1.76E-07
vg0509824684 sf0509824613 5 9824684 NA 5.12E-07
vg0808100775 sf0808099779 8 8100775 NA 1.18E-06
vg1214600105 sf1214597445 12 14600105 NA 2.33E-06
vg1004059501 sf1004058477 10 4059501 NA 3.50E-06