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 mr1982 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
vg1122020161 sf1121554032 11 22020161 2.44E-09 1.24E-06
vg0725674584 sf0725673590 7 25674584 3.87E-08 1.59E-06
vg1002388384 sf1002387361 10 2388384 5.89E-07 NA
vg1222295817 sf1222262364 12 22295817 1.15E-06 2.28E-07
vg0202518756 sf0202518754 2 2518756 1.49E-06 1.22E-06
vg0401253161 sf0401248711 4 1253161 7.06E-06 1.46E-06
vg1128779208 sf1128255987 11 28779208 NA 4.13E-06