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 mr1570 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
vg1001449111 sf1001448088 10 1449111 8.28E-11 6.06E-06
vg1001228707 sf1001227684 10 1228707 8.46E-11 3.62E-06
vg0908683286 sf0908682285 9 8683286 1.28E-10 NA
vg0611148454 sf0611147455 6 11148454 1.60E-10 3.75E-06
vg0611136921 sf0611135922 6 11136921 1.82E-10 2.31E-06
vg0724707548 sf0724706554 7 24707548 5.89E-10 NA
vg0414176940 sf0414167656 4 14176940 1.56E-09 NA
vg0324083524 sf0324081603 3 24083524 1.41E-07 2.45E-06