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 mr1912 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
vg1105925054 sf1105920806 11 5925054 7.73E-10 3.44E-06
vg0618179900 sf0618178903 6 18179900 3.12E-09 NA
vg1219173044 sf1219144514 12 19173044 3.90E-09 NA
vg1216470460 sf1216467753 12 16470460 8.49E-09 NA
vg0139829401 sf0139828358 1 39829401 1.08E-08 NA
vg0329617568 sf0329610608 3 29617568 3.82E-06 NA
vg0413385665 sf0413376376 4 13385665 4.77E-06 9.53E-07
vg0520358656 sf0520296129 5 20358656 NA 4.83E-08
vg1219121022 sf1219092458 12 19121022 NA 1.08E-06
vg0715317227 sf0715316234 7 15317227 NA 2.43E-06
vg1209159762 sf1209157171 12 9159762 NA 6.78E-06