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 mr1502 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
vg0221919301 sf0221913432 2 21919301 2.54E-11 9.37E-07
vg1217570924 sf1217564879 12 17570924 1.76E-10 NA
vg1023076399 sf1023004872 10 23076399 4.03E-10 NA
vg1118143847 sf1117677705 11 18143847 4.08E-10 NA
vg0132936830 sf0132935786 1 32936830 4.39E-10 NA
vg0102967856 sf0102966856 1 2967856 2.44E-08 NA
vg0419763927 sf0419591962 4 19763927 NA 9.03E-06