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 mr1124 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
vg0820812927 sf0820810214 8 20812927 3.26E-10 2.79E-07
vg0124176064 sf0124175020 1 24176064 2.61E-08 2.17E-08
vg0124173863 sf0124172819 1 24173863 3.32E-08 1.77E-08
vg1218161219 sf1218132655 12 18161219 3.57E-08 NA
vg0311437556 sf0311436274 3 11437556 3.68E-08 5.23E-06
vg0416883574 sf0416711616 4 16883574 4.64E-08 NA
vg0506583308 sf0506583249 5 6583308 1.21E-07 NA
vg0300180852 sf0300179852 3 180852 6.95E-07 3.53E-06
vg0820198596 sf0820195883 8 20198596 1.24E-06 2.18E-08
vg0421279302 sf0421107356 4 21279302 4.29E-06 NA
vg1003806408 sf1003805384 10 3806408 6.96E-06 2.10E-07
vg0917470581 sf0917469580 9 17470581 NA 1.61E-07
vg1212596614 sf1212593953 12 12596614 NA 1.63E-06
vg0820995250 sf0820992537 8 20995250 NA 1.93E-06
vg1220059260 sf1220030702 12 20059260 NA 2.05E-06
vg0432345183 sf0432160072 4 32345183 NA 2.58E-06
vg0121412555 sf0121411510 1 21412555 NA 3.03E-06
vg1226169508 sf1226135902 12 26169508 NA 3.69E-06
vg0618381087 sf0618380090 6 18381087 NA 4.81E-06