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 mr1243 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
vg0217739410 sf0217733540 2 17739410 2.54E-15 7.60E-11
vg0216662170 sf0216656300 2 16662170 1.03E-13 2.04E-08
vg0216664826 sf0216658956 2 16664826 1.74E-13 1.58E-08
vg0216756500 sf0216750630 2 16756500 3.81E-12 6.70E-07
vg1215868127 sf1215865423 12 15868127 2.08E-11 7.84E-06
vg1209702029 sf1209699438 12 9702029 2.51E-11 2.01E-06
vg1214140714 sf1214138054 12 14140714 4.52E-11 2.30E-07
vg1210412113 sf1210409526 12 10412113 5.33E-11 5.78E-07
vg0216865438 sf0216859568 2 16865438 2.58E-09 2.51E-06
vg0526296632 sf0526233995 5 26296632 1.64E-07 4.62E-06
vg0514184495 sf0514127039 5 14184495 1.40E-06 1.05E-06
vg1109530315 sf1109524892 11 9530315 1.52E-06 NA
vg0514011016 sf0513953560 5 14011016 4.84E-06 5.68E-06