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 mr1224 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
vg0719011406 sf0719010413 7 19011406 4.23E-20 1.30E-16
vg0719007567 sf0719006574 7 19007567 5.48E-20 2.27E-15
vg0222755345 sf0222749476 2 22755345 2.96E-12 1.28E-09
vg0719242112 sf0719241119 7 19242112 4.50E-10 4.24E-08
vg0719140315 sf0719139322 7 19140315 5.92E-10 3.10E-08
vg1201810312 sf1201809309 12 1810312 2.10E-08 NA
vg0724694719 sf0724693725 7 24694719 2.45E-08 3.06E-06
vg0305052881 sf0305051883 3 5052881 3.26E-08 1.99E-06
vg0724683198 sf0724682204 7 24683198 4.73E-08 2.43E-06
vg0719209824 sf0719208831 7 19209824 5.46E-08 2.36E-09
vg0718885795 sf0718884802 7 18885795 1.13E-07 1.76E-07
vg0719153233 sf0719152240 7 19153233 2.55E-07 1.50E-06
vg0719483130 sf0719482137 7 19483130 2.27E-06 3.35E-07
vg0719346699 sf0719345706 7 19346699 3.14E-06 4.30E-06
vg0208687924 sf0208687923 2 8687924 NA 4.84E-07
vg1204560575 sf1204559563 12 4560575 NA 1.22E-06
vg0119647380 sf0119646335 1 19647380 NA 2.19E-06
vg0622692751 sf0622691754 6 22692751 NA 4.51E-06
vg0110693719 sf0110692695 1 10693719 NA 4.57E-06