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 mr1534 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
vg0613477923 sf0613476924 6 13477923 9.51E-50 NA
vg0617880328 sf0617879331 6 17880328 1.33E-48 NA
vg0626679891 sf0626678894 6 26679891 5.87E-48 NA
vg0612943263 sf0612942264 6 12943263 3.79E-45 6.19E-07
vg0312494685 sf0312493403 3 12494685 5.18E-45 NA
vg0915536354 sf0915535353 9 15536354 3.47E-44 NA
vg0626719842 sf0626718845 6 26719842 3.43E-40 2.34E-06
vg0620767896 sf0620766899 6 20767896 1.05E-39 3.31E-08
vg0430605919 sf0430420794 4 30605919 NA 5.84E-13
vg1204313213 sf1204312201 12 4313213 NA 5.61E-08
vg0430612192 sf0430427067 4 30612192 NA 2.91E-07
vg0430479763 sf0430294641 4 30479763 NA 5.16E-07
vg1015945404 sf1015874175 10 15945404 NA 1.13E-06
vg1213804495 sf1213801833 12 13804495 NA 1.32E-06
vg1127845566 sf1127373952 11 27845566 NA 1.69E-06
vg0626719833 sf0626718836 6 26719833 NA 2.48E-06
vg0129240128 sf0129239083 1 29240128 NA 3.61E-06
vg0135555900 sf0135554857 1 35555900 NA 4.84E-06
vg0221843914 sf0221838045 2 21843914 NA 4.99E-06
vg0124877300 sf0124876256 1 24877300 NA 5.51E-06