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 mr1649 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
vg0217018976 sf0217013106 2 17018976 3.76E-10 7.86E-07
vg0216896614 sf0216890744 2 16896614 1.65E-09 1.58E-06
vg0216664283 sf0216658413 2 16664283 1.81E-09 5.69E-07
vg0216760944 sf0216755074 2 16760944 4.27E-09 NA
vg0907175571 sf0907174571 9 7175571 5.99E-07 NA
vg0334986236 sf0334979106 3 34986236 6.22E-07 8.11E-08
vg0820796944 sf0820794231 8 20796944 4.77E-06 4.61E-06
vg1215157972 sf1215155308 12 15157972 5.41E-06 NA
vg0334732696 sf0334725566 3 34732696 6.26E-06 5.63E-07
vg0327526492 sf0327519545 3 27526492 NA 3.65E-06