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 mr1061 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
vg0300265158 sf0300264158 3 265158 1.10E-07 1.10E-07
vg0819439794 sf0819437081 8 19439794 5.72E-07 5.73E-07
vg1219572926 sf1219544396 12 19572926 9.40E-07 9.37E-07
vg0127140857 sf0127139813 1 27140857 1.09E-06 1.09E-06
vg1218409904 sf1218381340 12 18409904 1.26E-06 1.26E-06
vg0421413370 sf0421241423 4 21413370 1.61E-06 1.61E-06
vg0431515534 sf0431330433 4 31515534 1.70E-06 1.70E-06
vg0132114572 sf0132113528 1 32114572 2.02E-06 2.02E-06
vg0719159480 sf0719158487 7 19159480 4.07E-06 4.08E-06
vg0125906058 sf0125905014 1 25906058 4.37E-06 4.38E-06