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 mr1494 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
vg0916577384 sf0916576383 9 16577384 7.22E-07 7.23E-07
vg0522014819 sf0521952261 5 22014819 2.24E-06 2.25E-06
vg1210660431 sf1210657844 12 10660431 2.37E-06 2.37E-06
vg0703879153 sf0703878154 7 3879153 3.04E-06 3.05E-06
vg0718817715 sf0718816722 7 18817715 3.29E-06 3.30E-06
vg0403054381 sf0403049985 4 3054381 3.61E-06 3.62E-06
vg0823786747 sf0823784033 8 23786747 4.05E-06 4.06E-06
vg0202529815 sf0202529813 2 2529815 4.48E-06 4.48E-06
vg1214008434 sf1214005774 12 14008434 6.30E-06 6.31E-06
vg0907668817 sf0907667817 9 7668817 7.18E-06 7.20E-06
vg0320942236 sf0320940746 3 20942236 7.88E-06 7.89E-06