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 mr1681 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
vg0324014449 sf0324012622 3 24014449 6.53E-10 1.87E-06
vg0618821836 sf0618820839 6 18821836 1.08E-09 7.48E-07
vg0618818863 sf0618817866 6 18818863 1.42E-09 9.97E-07
vg0402263999 sf0402259594 4 2263999 3.87E-09 5.90E-07
vg0501160825 sf0501160809 5 1160825 4.62E-09 NA
vg1219489547 sf1219461017 12 19489547 8.47E-09 NA
vg1218166040 sf1218137476 12 18166040 6.59E-08 NA
vg0324076908 sf0324074987 3 24076908 NA 1.60E-07