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 mr1363 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
vg0902581681 sf0902580681 9 2581681 3.32E-09 NA
vg0123658384 sf0123657340 1 23658384 3.86E-09 NA
vg0712288904 sf0712287911 7 12288904 5.61E-09 NA
vg0431298826 sf0431113716 4 31298826 9.09E-09 NA
vg0505835317 sf0505835255 5 5835317 9.82E-09 NA
vg0317372993 sf0317371803 3 17372993 2.57E-07 NA
vg0123461399 sf0123460355 1 23461399 8.25E-07 2.09E-06
vg0104863244 sf0104862244 1 4863244 1.52E-06 NA
vg1225764387 sf1225730781 12 25764387 NA 3.65E-06
vg0815185480 sf0815182766 8 15185480 NA 4.92E-06