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 mr1060 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
vg1122373396 sf1121907267 11 22373396 2.92E-07 2.92E-07
vg1218092121 sf1218063557 12 18092121 7.98E-07 7.98E-07
vg1000860638 sf1000859614 10 860638 1.82E-06 1.82E-06
vg0417168684 sf0416996725 4 17168684 2.79E-06 2.79E-06
vg1210401260 sf1210398673 12 10401260 3.47E-06 3.47E-06
vg0605351193 sf0605350194 6 5351193 5.38E-06 5.38E-06