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 mr1096 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
vg0610566343 sf0610565344 6 10566343 1.01E-51 1.89E-32
vg0610566084 sf0610565085 6 10566084 1.41E-50 1.28E-31
vg0612017410 sf0612016411 6 12017410 1.28E-16 2.32E-08
vg0610419183 sf0610418184 6 10419183 2.44E-16 3.04E-16
vg0610592410 sf0610591411 6 10592410 1.78E-15 1.62E-10
vg0611882368 sf0611881369 6 11882368 2.68E-15 1.40E-09
vg0616988304 sf0616987307 6 16988304 1.23E-14 4.54E-08
vg0610451701 sf0610450702 6 10451701 2.58E-14 3.65E-11
vg0610016274 sf0610015275 6 10016274 8.70E-12 1.54E-09
vg0610684751 sf0610683752 6 10684751 2.09E-11 5.69E-07
vg0610556004 sf0610555005 6 10556004 4.53E-11 1.39E-08
vg0610752419 sf0610751420 6 10752419 7.48E-10 2.19E-07
vg0611466166 sf0611465167 6 11466166 3.32E-09 8.94E-07
vg0610442142 sf0610441143 6 10442142 4.24E-09 3.91E-07
vg0610636368 sf0610635369 6 10636368 1.64E-08 1.14E-06
vg0613062563 sf0613061564 6 13062563 3.23E-08 7.93E-07
vg0610116533 sf0610115534 6 10116533 4.47E-08 9.38E-07
vg0615150907 sf0615149908 6 15150907 1.37E-07 1.55E-06
vg0610820708 sf0610819709 6 10820708 1.12E-06 1.65E-08
vg0414588084 sf0414578798 4 14588084 1.26E-06 NA
vg0610752378 sf0610751379 6 10752378 NA 9.91E-08
vg0124058988 sf0124057944 1 24058988 NA 3.77E-07
vg0122730287 sf0122729243 1 22730287 NA 6.36E-07
vg0612288311 sf0612287312 6 12288311 NA 9.09E-07
vg0611255073 sf0611254074 6 11255073 NA 1.04E-06