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 mr1721 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
vg0232027520 sf0232021651 2 32027520 5.27E-48 8.15E-07
vg0232211159 sf0232205290 2 32211159 1.07E-47 6.97E-08
vg0717311708 sf0717310715 7 17311708 6.04E-47 NA
vg0229369214 sf0229363345 2 29369214 7.27E-47 NA
vg0308724662 sf0308723600 3 8724662 1.03E-46 NA
vg0702551779 sf0702550780 7 2551779 1.10E-46 NA
vg1001395945 sf1001394922 10 1395945 NA 6.48E-09
vg1001388777 sf1001387754 10 1388777 NA 7.28E-09
vg1001388587 sf1001387564 10 1388587 NA 1.79E-08
vg0232357463 sf0232351594 2 32357463 NA 6.27E-07
vg1000942377 sf1000941353 10 942377 NA 1.08E-06
vg1001428880 sf1001427857 10 1428880 NA 1.59E-06
vg0701714318 sf0701713319 7 1714318 NA 2.19E-06
vg0806066076 sf0806065081 8 6066076 NA 2.22E-06
vg1118796541 sf1118330349 11 18796541 NA 4.16E-06
vg0801523305 sf0801522307 8 1523305 NA 4.84E-06