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 mr1380 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
vg0123467869 sf0123466825 1 23467869 1.91E-14 2.75E-06
vg1126984434 sf1126512821 11 26984434 4.00E-13 NA
vg0619445566 sf0619444569 6 19445566 1.88E-12 NA
vg0307489962 sf0307488900 3 7489962 3.71E-12 NA
vg1125786354 sf1125320275 11 25786354 4.17E-12 1.11E-06
vg0300483843 sf0300482841 3 483843 1.27E-11 2.55E-06
vg1126496401 sf1126024815 11 26496401 3.54E-11 8.36E-10
vg0122431110 sf0122430065 1 22431110 4.14E-10 5.43E-06
vg0123073132 sf0123072088 1 23073132 3.40E-07 NA
vg0516005213 sf0515947721 5 16005213 1.99E-06 NA
vg0123335316 sf0123334272 1 23335316 6.09E-06 2.30E-06
vg1101201264 sf1101200265 11 1201264 NA 6.95E-07
vg1101142475 sf1101141476 11 1142475 NA 2.58E-06
vg0233057746 sf0233051877 2 33057746 NA 2.63E-06