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 mr1655 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
vg0516673461 sf0516613103 5 16673461 5.83E-10 NA
vg0232208358 sf0232202489 2 32208358 1.01E-09 4.50E-06
vg0904256580 sf0904255580 9 4256580 2.46E-09 NA
vg0701498071 sf0701497071 7 1498071 3.89E-09 NA
vg0716746513 sf0716745520 7 16746513 5.44E-09 NA
vg0203358788 sf0203358786 2 3358788 1.48E-08 3.19E-06
vg1208604811 sf1208602218 12 8604811 2.55E-08 4.79E-06
vg0420664918 sf0420492961 4 20664918 6.04E-08 4.09E-06
vg0516302066 sf0516244548 5 16302066 6.88E-08 8.33E-06
vg0516563624 sf0516506106 5 16563624 9.21E-08 1.51E-06
vg0420376308 sf0420204352 4 20376308 5.24E-06 NA
vg0431043984 sf0430858869 4 31043984 NA 6.59E-07