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 mr1794 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
vg1009133110 sf1009061971 10 9133110 1.34E-22 1.54E-09
vg1006717054 sf1006732677 10 6717054 6.18E-21 1.09E-09
vg1006382038 sf1006397661 10 6382038 7.31E-21 2.53E-08
vg1007756402 sf1007772012 10 7756402 3.91E-19 3.72E-08
vg1008310948 sf1008239810 10 8310948 4.77E-19 9.53E-09
vg0407822256 sf0407817524 4 7822256 3.52E-18 2.48E-06
vg1202107576 sf1202106574 12 2107576 3.77E-18 7.78E-06
vg0407822984 sf0407818252 4 7822984 4.40E-18 1.98E-06
vg0905249361 sf0905248361 9 5249361 2.70E-17 4.54E-06
vg0222739831 sf0222733962 2 22739831 3.41E-14 2.97E-07
vg0222721955 sf0222716086 2 22721955 1.88E-12 1.96E-07
vg1207709184 sf1207706588 12 7709184 8.69E-12 2.52E-06
vg1118364611 sf1117898469 11 18364611 9.57E-12 2.27E-06
vg0525591460 sf0525528881 5 25591460 NA 8.62E-07
vg1128863835 sf1128340614 11 28863835 NA 1.57E-06
vg0826134475 sf0826131761 8 26134475 NA 3.76E-06
vg0122199419 sf0122198374 1 22199419 NA 9.09E-06