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 mr1897 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
vg0216982985 sf0216977115 2 16982985 3.07E-14 3.07E-14
vg0216988231 sf0216982361 2 16988231 6.26E-13 6.26E-13
vg0210828426 sf0210828424 2 10828426 2.52E-08 2.52E-08
vg0507443101 sf0507443043 5 7443101 5.48E-08 5.48E-08
vg0209641266 sf0209641264 2 9641266 2.11E-07 2.11E-07
vg0218547738 sf0218541869 2 18547738 2.96E-07 2.96E-07
vg0319337674 sf0319336185 3 19337674 1.53E-06 1.53E-06
vg0400239462 sf0400238462 4 239462 3.01E-06 3.01E-06