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 mr1188 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
vg0906561460 sf0906560460 9 6561460 9.04E-10 2.12E-06
vg0106538346 sf0106537346 1 6538346 1.03E-09 NA
vg0824108010 sf0824105296 8 24108010 1.10E-09 NA
vg0414628053 sf0414618767 4 14628053 1.45E-09 NA
vg0324923610 sf0324921690 3 24923610 1.45E-09 NA
vg0142615783 sf0142614739 1 42615783 2.74E-09 NA
vg0313981935 sf0313980652 3 13981935 1.94E-08 NA
vg0723827164 sf0723826170 7 23827164 5.52E-08 1.02E-07
vg0431494115 sf0431309014 4 31494115 9.83E-08 2.56E-06
vg0309108474 sf0309107410 3 9108474 1.40E-07 NA
vg0404929690 sf0404925129 4 4929690 2.24E-06 NA