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 mr1927 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
vg0217109099 sf0217103229 2 17109099 9.37E-25 2.00E-17
vg0217093619 sf0217087749 2 17093619 3.11E-24 9.78E-18
vg0217112842 sf0217106972 2 17112842 4.95E-23 6.06E-12
vg0216995459 sf0216989589 2 16995459 9.25E-23 1.71E-12
vg0631227245 sf0631226247 6 31227245 2.48E-15 NA
vg0133840259 sf0133839215 1 33840259 2.79E-15 NA
vg0719534510 sf0719533517 7 19534510 4.58E-14 NA
vg1220336354 sf1220307796 12 20336354 2.77E-12 3.43E-06
vg0107834437 sf0107833437 1 7834437 4.82E-12 3.95E-06
vg0217835710 sf0217829841 2 17835710 6.80E-12 3.37E-09
vg0907107754 sf0907106754 9 7107754 1.02E-10 NA
vg1017014524 sf1016943296 10 17014524 1.48E-10 4.69E-06
vg0217594477 sf0217588607 2 17594477 2.04E-10 5.84E-08
vg0415966817 sf0415794850 4 15966817 3.62E-10 NA
vg0611539103 sf0611538104 6 11539103 4.52E-10 NA
vg0217125798 sf0217119928 2 17125798 NA 5.41E-10
vg1128516527 sf1127993306 11 28516527 NA 1.98E-07
vg1108225523 sf1108220133 11 8225523 NA 3.34E-07
vg0217595430 sf0217589560 2 17595430 NA 3.64E-07
vg0217430075 sf0217424205 2 17430075 NA 6.38E-07
vg0518016012 sf0517955498 5 18016012 NA 8.03E-07
vg0516403916 sf0516346398 5 16403916 NA 9.93E-07
vg0216650070 sf0216644200 2 16650070 NA 3.11E-06
vg0907138440 sf0907137440 9 7138440 NA 3.54E-06