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 mr1268 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
vg0138103681 sf0138102638 1 38103681 1.53E-14 NA
vg0133604167 sf0133603123 1 33604167 3.53E-13 NA
vg0133342600 sf0133341556 1 33342600 3.46E-12 NA
vg0129214554 sf0129213509 1 29214554 4.35E-11 NA
vg0123683673 sf0123682629 1 23683673 4.81E-10 NA
vg0603198141 sf0603197142 6 3198141 5.00E-10 NA
vg0921007352 sf0921006871 9 21007352 5.03E-10 4.05E-06
vg0626912201 sf0626911204 6 26912201 7.08E-08 2.97E-06
vg0100674416 sf0100673416 1 674416 7.18E-08 NA
vg0519021172 sf0518958656 5 19021172 1.27E-07 4.94E-06
vg0206506462 sf0206393560 2 6506462 4.34E-06 NA