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 mr1953 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
vg0118269761 sf0118268715 1 18269761 1.22E-07 1.23E-07
vg1214822308 sf1214819649 12 14822308 2.15E-07 2.16E-07
vg0905354568 sf0905353568 9 5354568 3.67E-07 3.69E-07
vg1214134657 sf1214131997 12 14134657 5.96E-07 5.97E-07
vg0719334703 sf0719333710 7 19334703 8.96E-07 8.99E-07
vg0431515534 sf0431330433 4 31515534 1.05E-06 1.05E-06
vg0320043666 sf0320042177 3 20043666 1.49E-06 1.50E-06
vg0115532707 sf0115531681 1 15532707 2.61E-06 2.62E-06
vg0715489455 sf0715488462 7 15489455 3.51E-06 3.52E-06
vg0218622148 sf0218616279 2 18622148 3.79E-06 3.80E-06
vg0200505558 sf0200505558 2 505558 3.90E-06 3.91E-06
vg1219572926 sf1219544396 12 19572926 7.85E-06 7.81E-06