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 mr1533 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
vg1013484683 sf1013413453 10 13484683 7.93E-31 4.73E-15
vg1013543098 sf1013471868 10 13543098 4.06E-29 1.58E-15
vg0608463692 sf0608462693 6 8463692 2.70E-18 2.06E-06
vg0315364439 sf0315363086 3 15364439 1.77E-16 NA
vg0122205444 sf0122204399 1 22205444 1.95E-15 NA
vg1016159070 sf1016087842 10 16159070 2.18E-15 NA
vg0817829169 sf0817826456 8 17829169 3.65E-14 2.99E-06
vg0920403296 sf0920402815 9 20403296 3.47E-12 1.24E-06