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 mr1480 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
vg0718144114 sf0718143121 7 18144114 1.28E-07 6.94E-07
vg0718133718 sf0718132725 7 18133718 1.46E-07 3.65E-06
vg0703673198 sf0703672199 7 3673198 1.88E-07 1.58E-07
vg0104049262 sf0104048262 1 4049262 2.21E-07 2.99E-06
vg0716241220 sf0716240227 7 16241220 3.04E-07 2.26E-06
vg0205305322 sf0205305321 2 5305322 7.72E-07 2.97E-06
vg0718910920 sf0718909927 7 18910920 1.15E-06 9.26E-07