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 mr1173 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
vg1207884606 sf1207882012 12 7884606 3.15E-08 3.15E-08
vg1116054140 sf1115589012 11 16054140 6.26E-07 6.26E-07
vg0507078625 sf0507078567 5 7078625 9.44E-07 9.44E-07
vg0210662977 sf0210662975 2 10662977 3.37E-06 3.37E-06
vg0808350901 sf0808349905 8 8350901 3.41E-06 3.41E-06
vg1010194791 sf1010123612 10 10194791 4.06E-06 4.06E-06
vg0916032111 sf0916031110 9 16032111 4.08E-06 4.08E-06
vg1013279779 sf1013208548 10 13279779 4.36E-06 4.36E-06
vg0604305997 sf0604304998 6 4305997 4.95E-06 4.95E-06
vg1107414104 sf1107409849 11 7414104 7.60E-06 7.60E-06