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 mr1582 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
vg1217924507 sf1217895941 12 17924507 5.40E-07 5.40E-07
vg0604305985 sf0604304986 6 4305985 1.10E-06 1.10E-06
vg1009290716 sf1009219537 10 9290716 1.21E-06 1.21E-06
vg1208769199 sf1208766606 12 8769199 1.34E-06 1.34E-06
vg0604311698 sf0604310699 6 4311698 1.41E-06 1.41E-06
vg0708261838 sf0708260843 7 8261838 1.57E-06 1.57E-06
vg1118022184 sf1117556042 11 18022184 2.98E-06 2.97E-06
vg1206392661 sf1206391551 12 6392661 5.01E-06 5.01E-06