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 mr1688 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
vg0420718113 sf0420546156 4 20718113 1.25E-07 1.25E-07
vg0808428148 sf0808427152 8 8428148 2.94E-07 2.94E-07
vg1020531763 sf1020460242 10 20531763 4.91E-07 4.90E-07
vg0516508609 sf0516451091 5 16508609 6.58E-07 6.57E-07
vg0220342715 sf0220336847 2 20342715 1.09E-06 1.09E-06
vg1020529341 sf1020457820 10 20529341 1.48E-06 1.48E-06
vg0142427760 sf0142426716 1 42427760 2.17E-06 2.17E-06
vg0500918476 sf0500918459 5 918476 4.17E-06 4.17E-06
vg0726559146 sf0726558152 7 26559146 4.31E-06 4.31E-06
vg0630359504 sf0630358506 6 30359504 4.52E-06 4.52E-06
vg0607659813 sf0607658814 6 7659813 4.53E-06 4.50E-06