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 mr1896 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
vg0524494561 sf0524431982 5 24494561 3.73E-103 3.73E-22
vg0524593054 sf0524530474 5 24593054 1.57E-100 2.17E-22
vg1209153210 sf1209150619 12 9153210 3.56E-73 NA
vg0232358240 sf0232352371 2 32358240 3.76E-70 NA
vg0129939389 sf0129938344 1 29939389 9.97E-70 NA
vg0317818639 sf0317817421 3 17818639 7.28E-69 NA
vg0524793384 sf0524730799 5 24793384 NA 4.17E-12
vg0524300922 sf0524238341 5 24300922 NA 5.16E-07
vg0101328049 sf0101327049 1 1328049 NA 5.93E-07
vg0726131769 sf0726130775 7 26131769 NA 1.27E-06
vg0229918162 sf0229912293 2 29918162 NA 1.56E-06
vg0216878747 sf0216872877 2 16878747 NA 1.65E-06
vg0141183119 sf0141182076 1 41183119 NA 1.82E-06
vg0301847279 sf0301846275 3 1847279 NA 2.51E-06
vg1012107605 sf1012036420 10 12107605 NA 2.72E-06
vg0427084332 sf0426899204 4 27084332 NA 2.99E-06
vg0624529099 sf0624528102 6 24529099 NA 4.10E-06
vg0306212740 sf0306211740 3 6212740 NA 4.49E-06