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 mr1088 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
vg0719055987 sf0719054994 7 19055987 6.67E-19 8.97E-18
vg0809549221 sf0809548225 8 9549221 1.89E-07 2.90E-06
vg0520022893 sf0519960369 5 20022893 4.11E-07 3.34E-06
vg0820065663 sf0820062950 8 20065663 7.96E-07 2.69E-06
vg0702575490 sf0702574491 7 2575490 1.03E-06 4.16E-06
vg0719053396 sf0719052403 7 19053396 NA 6.95E-08