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 mr1829 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
vg0331280409 sf0331273294 3 31280409 9.25E-41 2.46E-23
vg1115457697 sf1114994009 11 15457697 2.06E-14 NA
vg0331370140 sf0331363025 3 31370140 4.62E-14 1.87E-06
vg0329570872 sf0329563912 3 29570872 5.23E-14 9.98E-07
vg0329570929 sf0329563969 3 29570929 5.54E-14 4.13E-07
vg1111156033 sf1111150350 11 11156033 1.96E-13 NA
vg1020873245 sf1020801724 10 20873245 1.58E-11 2.03E-07
vg0700231073 sf0700230073 7 231073 1.96E-09 2.00E-06
vg1216532803 sf1216530096 12 16532803 2.44E-08 1.51E-06
vg0522891091 sf0522828533 5 22891091 NA 8.44E-07
vg0504908967 sf0504908945 5 4908967 NA 1.12E-06
vg0419547373 sf0419375411 4 19547373 NA 1.86E-06
vg0114496693 sf0114495667 1 14496693 NA 4.79E-06
vg0139756216 sf0139755173 1 39756216 NA 5.86E-06