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 mr1784 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
vg0722493510 sf0722492517 7 22493510 2.48E-07 2.48E-07
vg0329917563 sf0329910602 3 29917563 1.06E-06 1.06E-06
vg0128120219 sf0128119175 1 28120219 2.10E-06 2.10E-06
vg0432540222 sf0432355114 4 32540222 2.20E-06 2.20E-06
vg0128078547 sf0128077503 1 28078547 2.85E-06 2.85E-06
vg0519675004 sf0519612488 5 19675004 2.96E-06 2.96E-06