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 mr1622 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
vg1211581493 sf1211578829 12 11581493 2.51E-08 NA
vg0818525912 sf0818523199 8 18525912 2.77E-08 9.07E-07
vg0826832590 sf0826829876 8 26832590 4.16E-08 NA
vg1006980661 sf1006996284 10 6980661 4.37E-08 NA
vg0226447825 sf0226441956 2 26447825 9.59E-08 NA
vg1102499895 sf1102495799 11 2499895 2.59E-07 1.84E-06
vg1006295271 sf1006310894 10 6295271 4.99E-06 NA