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 mr1630 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
vg0501153947 sf0501153931 5 1153947 7.67E-08 3.59E-06
vg0122689969 sf0122688924 1 22689969 9.00E-08 2.31E-07
vg1214592827 sf1214590167 12 14592827 5.66E-07 3.42E-06
vg1220408794 sf1220380236 12 20408794 2.06E-06 4.63E-06
vg0500173356 sf0500173356 5 173356 4.62E-06 NA
vg0420190638 sf0420018678 4 20190638 6.79E-06 NA
vg0917631772 sf0917630771 9 17631772 NA 6.45E-07
vg1218108461 sf1218079897 12 18108461 NA 6.71E-07