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 mr1361 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
vg0313147221 sf0313145939 3 13147221 2.75E-14 1.87E-06
vg1020120628 sf1020049126 10 20120628 4.82E-14 1.27E-06
vg0728551617 sf0728550625 7 28551617 6.79E-14 4.97E-06
vg1020039082 sf1019967580 10 20039082 3.06E-13 6.97E-07
vg0816117066 sf0816114352 8 16117066 8.79E-13 NA
vg0919529939 sf0919529529 9 19529939 2.95E-12 NA
vg1102677343 sf1102673247 11 2677343 4.63E-10 1.18E-06