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 mr1175 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
vg0232693982 sf0232688113 2 32693982 9.45E-14 NA
vg0112931554 sf0112930528 1 12931554 3.29E-13 3.07E-06
vg0613879682 sf0613878683 6 13879682 3.32E-13 NA
vg0206301171 sf0206301171 2 6301171 4.90E-13 NA
vg0139831720 sf0139830677 1 39831720 1.03E-12 NA
vg0113106800 sf0113105774 1 13106800 3.73E-12 8.91E-06
vg0716948952 sf0716947959 7 16948952 3.74E-11 NA
vg0230185057 sf0230179188 2 30185057 6.95E-11 NA
vg0723915705 sf0723914711 7 23915705 NA 1.07E-06