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 mr1745 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
vg1125263550 sf1124797390 11 25263550 2.36E-12 1.32E-07
vg1125257892 sf1124791732 11 25257892 2.77E-10 3.81E-07
vg0305058156 sf0305057158 3 5058156 4.18E-09 NA
vg0325647845 sf0325645863 3 25647845 8.68E-09 3.99E-07
vg1017173869 sf1017102642 10 17173869 1.52E-08 3.25E-07
vg0105042933 sf0105041933 1 5042933 1.83E-08 NA
vg0918621961 sf0918620960 9 18621961 7.09E-08 8.68E-07
vg1017150631 sf1017079403 10 17150631 1.25E-07 3.55E-07
vg1121167517 sf1120701396 11 21167517 1.87E-07 4.75E-06
vg0400771729 sf0400770729 4 771729 2.60E-07 1.40E-08
vg0118034244 sf0118033198 1 18034244 5.64E-07 1.27E-07
vg1217503845 sf1217497800 12 17503845 3.93E-06 4.95E-06
vg0329925779 sf0329918818 3 29925779 3.93E-06 3.83E-06
vg0622648138 sf0622647141 6 22648138 NA 3.66E-06
vg1104295772 sf1104291674 11 4295772 NA 4.42E-06
vg0427684784 sf0427499647 4 27684784 NA 4.98E-06