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 mr1817 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
vg0919912392 sf0919911911 9 19912392 1.09E-23 2.62E-06
vg0825539010 sf0825536296 8 25539010 4.02E-22 7.63E-06
vg0904124928 sf0904123928 9 4124928 4.42E-22 NA
vg0900796344 sf0900795344 9 796344 5.24E-22 NA
vg1015210569 sf1015139337 10 15210569 1.16E-21 NA
vg0920103821 sf0920103340 9 20103821 4.10E-20 1.78E-06
vg0617030325 sf0617029328 6 17030325 1.47E-17 NA
vg0700675337 sf0700674337 7 675337 NA 8.51E-07
vg1015204035 sf1015132803 10 15204035 NA 1.03E-06
vg0904767635 sf0904766635 9 4767635 NA 2.64E-06
vg0225867144 sf0225861275 2 25867144 NA 3.11E-06
vg0631079165 sf0631078167 6 31079165 NA 3.30E-06