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 mr1851 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
vg0142873796 sf0142872752 1 42873796 1.08E-06 3.17E-07
vg1114618741 sf1114155059 11 14618741 1.58E-06 9.15E-06
vg0826647284 sf0826644570 8 26647284 2.25E-06 3.58E-06
vg0418589258 sf0418417303 4 18589258 2.69E-06 1.24E-06
vg0418762339 sf0418590384 4 18762339 4.02E-06 6.16E-07
vg0403055835 sf0403051439 4 3055835 6.88E-06 3.32E-06