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 mr1415 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
vg1102677343 sf1102673247 11 2677343 5.06E-09 2.03E-07
vg1215099338 sf1215096675 12 15099338 4.58E-08 2.45E-06
vg0921095515 sf0921095034 9 21095515 9.43E-08 1.26E-06
vg1213717956 sf1213715294 12 13717956 2.05E-07 2.10E-06
vg1004654280 sf1004670817 10 4654280 3.12E-07 3.83E-06
vg1000803065 sf1000802041 10 803065 6.12E-07 2.97E-06
vg1204324619 sf1204323607 12 4324619 2.34E-06 3.54E-06