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 mr1519 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
vg0115224388 sf0115223362 1 15224388 1.58E-57 6.41E-06
vg0109389615 sf0109388591 1 9389615 1.79E-55 6.83E-08
vg0117972404 sf0117971358 1 17972404 3.52E-54 NA
vg0822986617 sf0822983904 8 22986617 3.89E-52 NA
vg0917914071 sf0917913070 9 17914071 1.08E-51 NA
vg0115499545 sf0115498519 1 15499545 NA 5.00E-11
vg0114684305 sf0114683279 1 14684305 NA 9.58E-08
vg0814797975 sf0814795261 8 14797975 NA 4.03E-07
vg0804502899 sf0804501902 8 4502899 NA 4.27E-07
vg0119718756 sf0119717711 1 19718756 NA 6.21E-07
vg0118743986 sf0118742940 1 18743986 NA 1.26E-06
vg1218071776 sf1218043212 12 18071776 NA 1.28E-06
vg0334627622 sf0334620492 3 34627622 NA 1.96E-06
vg0115342747 sf0115341721 1 15342747 NA 2.00E-06
vg0119924762 sf0119923717 1 19924762 NA 2.55E-06
vg0906315696 sf0906314696 9 6315696 NA 3.67E-06
vg0311016054 sf0311014772 3 11016054 NA 4.13E-06
vg0816228377 sf0816225663 8 16228377 NA 4.76E-06
vg1218016436 sf1217987872 12 18016436 NA 8.72E-06