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 mr1410 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
vg0408294814 sf0408290088 4 8294814 3.43E-19 6.54E-10
vg1214370012 sf1214367353 12 14370012 3.26E-16 1.27E-08
vg0215909137 sf0215903267 2 15909137 1.77E-15 NA
vg1210300519 sf1210297932 12 10300519 2.58E-15 1.06E-08
vg0504497819 sf0504497796 5 4497819 1.02E-14 2.03E-09
vg1219311447 sf1219282917 12 19311447 1.43E-14 1.28E-06
vg0613566824 sf0613565825 6 13566824 4.98E-13 1.30E-06
vg0618522104 sf0618521107 6 18522104 1.86E-12 3.48E-07
vg0217670144 sf0217664274 2 17670144 4.12E-12 2.30E-06
vg0806335787 sf0806334792 8 6335787 3.32E-10 3.99E-06
vg0618479382 sf0618478385 6 18479382 5.89E-10 NA
vg0718523777 sf0718522784 7 18523777 6.83E-10 6.89E-07
vg0920014915 sf0920014434 9 20014915 2.70E-09 1.86E-07
vg0517964915 sf0517904401 5 17964915 1.04E-08 NA
vg0721118397 sf0721117404 7 21118397 1.87E-08 4.40E-06
vg1003300020 sf1003298997 10 3300020 NA 9.67E-07
vg1116343038 sf1115877914 11 16343038 NA 1.31E-06
vg0702242561 sf0702241562 7 2242561 NA 2.58E-06
vg1005989184 sf1006005722 10 5989184 NA 3.03E-06
vg0405830051 sf0405825490 4 5830051 NA 3.41E-06