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 mr1862 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
vg1018401992 sf1018330549 10 18401992 1.97E-12 2.61E-07
vg0216512359 sf0216506489 2 16512359 7.91E-11 NA
vg0515318112 sf0515260653 5 15318112 1.05E-10 9.92E-06
vg0802714869 sf0802713872 8 2714869 5.35E-10 NA
vg0128103219 sf0128102175 1 28103219 1.34E-09 NA
vg0109188806 sf0109187806 1 9188806 NA 6.22E-07