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 mr1230 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
vg1213717963 sf1213715301 12 13717963 1.69E-07 1.69E-07
vg1102677343 sf1102673247 11 2677343 7.52E-07 7.52E-07
vg0125628571 sf0125627527 1 25628571 9.53E-07 9.53E-07
vg0902893640 sf0902892640 9 2893640 1.08E-06 1.08E-06
vg0418087588 sf0417915629 4 18087588 1.45E-06 1.45E-06
vg0921699962 sf0921699481 9 21699962 3.09E-06 3.09E-06
vg1000803065 sf1000802041 10 803065 3.93E-06 3.93E-06
vg0217857667 sf0217851798 2 17857667 4.05E-06 4.05E-06