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 mr1202 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
vg0222745198 sf0222739329 2 22745198 1.16E-66 2.98E-26
vg0222725103 sf0222719234 2 22725103 5.22E-66 2.74E-26
vg0705482686 sf0705481687 7 5482686 2.23E-33 NA
vg0715689711 sf0715688718 7 15689711 1.09E-32 NA
vg0626744652 sf0626743655 6 26744652 1.58E-32 NA
vg0617630769 sf0617629772 6 17630769 1.92E-32 NA
vg0222857256 sf0222851387 2 22857256 4.57E-29 3.17E-07
vg0222725003 sf0222719134 2 22725003 NA 8.34E-11
vg0224553122 sf0224547253 2 24553122 NA 5.50E-08
vg0224275719 sf0224269850 2 24275719 NA 7.03E-07
vg0118115278 sf0118114232 1 18115278 NA 8.22E-07
vg0421072597 sf0420900652 4 21072597 NA 9.44E-07
vg0224508339 sf0224502470 2 24508339 NA 1.03E-06
vg0809991680 sf0809990684 8 9991680 NA 1.62E-06
vg0220187125 sf0220181257 2 20187125 NA 2.08E-06
vg0224242852 sf0224236983 2 24242852 NA 3.13E-06
vg0223537448 sf0223531579 2 23537448 NA 3.93E-06
vg0715115605 sf0715114612 7 15115605 NA 4.47E-06