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 mr1732 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
vg0520082492 sf0520019968 5 20082492 2.30E-24 NA
vg1000839305 sf1000838281 10 839305 5.45E-23 NA
vg0122975265 sf0122974221 1 22975265 8.50E-23 NA
vg1125433497 sf1124967336 11 25433497 8.76E-22 1.54E-06
vg0529405800 sf0529343155 5 29405800 2.03E-21 NA
vg0129933965 sf0129932920 1 29933965 1.01E-19 6.80E-07
vg0129868849 sf0129867804 1 29868849 2.68E-17 1.29E-07
vg0314829204 sf0314827851 3 14829204 8.47E-16 3.34E-07
vg1125475428 sf1125009267 11 25475428 5.78E-15 2.56E-08
vg1016929873 sf1016858645 10 16929873 3.40E-14 2.37E-06
vg1003063551 sf1003062528 10 3063551 4.52E-13 9.05E-07
vg1122053907 sf1121587778 11 22053907 1.21E-12 3.83E-06
vg1002992765 sf1002991742 10 2992765 NA 6.85E-07
vg0713262354 sf0713261361 7 13262354 NA 1.48E-06
vg0312540667 sf0312539385 3 12540667 NA 1.79E-06
vg0122690936 sf0122689891 1 22690936 NA 2.40E-06
vg1127574467 sf1127102854 11 27574467 NA 3.60E-06
vg0110837074 sf0110836050 1 10837074 NA 4.49E-06