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 mr1172 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
vg0127410771 sf0127409727 1 27410771 3.69E-07 3.69E-07
vg0827152045 sf0827149331 8 27152045 4.02E-07 4.02E-07
vg0111800114 sf0111799088 1 11800114 7.57E-07 7.57E-07
vg1102244084 sf1102239942 11 2244084 2.24E-06 2.24E-06
vg0224723022 sf0224717153 2 24723022 2.49E-06 2.49E-06
vg1127578048 sf1127106435 11 27578048 2.68E-06 2.68E-06
vg0806378465 sf0806377470 8 6378465 3.07E-06 3.07E-06
vg0724466415 sf0724465421 7 24466415 3.58E-06 3.58E-06
vg0107648672 sf0107647672 1 7648672 4.29E-06 4.29E-06
vg1202351626 sf1202350627 12 2351626 6.67E-06 6.67E-06