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 mr1202 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
vg0118115278 sf0118114232 1 18115278 1.59E-09 2.64E-06
vg0135555900 sf0135554857 1 35555900 1.61E-09 6.71E-06
vg0824722894 sf0824720180 8 24722894 2.10E-09 NA
vg0115542560 sf0115541534 1 15542560 2.88E-09 4.90E-06
vg0132176925 sf0132175881 1 32176925 4.50E-09 NA
vg0121412555 sf0121411510 1 21412555 NA 2.15E-06