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 mr1749 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
vg0911893007 sf0911892006 9 11893007 7.61E-09 NA
vg1218127441 sf1218098877 12 18127441 5.45E-08 NA
vg0414335944 sf0414326657 4 14335944 8.32E-08 NA
vg0515273812 sf0515216353 5 15273812 6.41E-07 NA
vg0611582868 sf0611581869 6 11582868 9.39E-07 6.68E-06
vg0519573025 sf0519510509 5 19573025 1.06E-06 NA
vg1220908877 sf1220875426 12 20908877 1.68E-06 NA
vg0113849031 sf0113848005 1 13849031 2.75E-06 NA