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 mr1864 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
vg0419220060 sf0419048098 4 19220060 5.83E-45 2.22E-29
vg0810545060 sf0810544064 8 10545060 1.03E-16 NA
vg0425494396 sf0425309256 4 25494396 8.65E-16 NA
vg0414049293 sf0414040008 4 14049293 1.16E-15 NA
vg1219410269 sf1219381739 12 19410269 1.51E-15 NA
vg0815339015 sf0815336301 8 15339015 1.55E-14 4.66E-06
vg0419261408 sf0419089446 4 19261408 2.39E-13 4.06E-06
vg0419205007 sf0419033043 4 19205007 NA 8.91E-11
vg0419244242 sf0419072280 4 19244242 NA 2.12E-10
vg0815133904 sf0815131190 8 15133904 NA 8.00E-07
vg0421019575 sf0420847628 4 21019575 NA 1.61E-06
vg0402781867 sf0402777472 4 2781867 NA 1.82E-06
vg0906127537 sf0906126537 9 6127537 NA 3.25E-06
vg0417784069 sf0417612106 4 17784069 NA 4.55E-06