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 mr1277 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
vg0800313711 sf0800312711 8 313711 1.03E-25 1.19E-12
vg0800302779 sf0800301779 8 302779 9.64E-25 1.32E-14
vg0128147365 sf0128146321 1 28147365 2.51E-21 NA
vg0804124681 sf0804123684 8 4124681 2.01E-20 NA
vg0800402228 sf0800401228 8 402228 6.04E-20 2.08E-07
vg0113855432 sf0113854406 1 13855432 8.62E-20 NA
vg0602854153 sf0602853154 6 2854153 2.02E-15 NA
vg0431858725 sf0431673619 4 31858725 2.36E-15 NA
vg0800413021 sf0800412021 8 413021 NA 6.99E-11
vg0800452335 sf0800451335 8 452335 NA 6.89E-10
vg0800225034 sf0800224034 8 225034 NA 1.80E-09
vg0800433392 sf0800432392 8 433392 NA 3.84E-07
vg0800100200 sf0800099200 8 100200 NA 1.23E-06
vg0800266718 sf0800265718 8 266718 NA 1.40E-06
vg0417872342 sf0417700384 4 17872342 NA 4.85E-06