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 mr1153 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
vg0119598439 sf0119597394 1 19598439 6.76E-08 6.77E-08
vg0431498650 sf0431313549 4 31498650 2.92E-07 2.92E-07
vg0718838390 sf0718837397 7 18838390 3.03E-07 3.03E-07
vg0820534605 sf0820531892 8 20534605 6.74E-07 6.74E-07
vg0207854825 sf0207854824 2 7854825 9.31E-07 9.31E-07
vg1105281315 sf1105277066 11 5281315 9.51E-07 9.51E-07
vg0119838948 sf0119837903 1 19838948 1.78E-06 1.78E-06
vg1104978992 sf1104974803 11 4978992 2.62E-06 2.62E-06
vg0820919871 sf0820917158 8 20919871 4.16E-06 4.16E-06