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 mr1884 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 5.60E-09 3.17E-07
vg1215482015 sf1215479312 12 15482015 1.40E-08 1.18E-06
vg0403315819 sf0403311422 4 3315819 2.81E-08 3.68E-07
vg1213717963 sf1213715301 12 13717963 3.07E-08 5.43E-07
vg1213717956 sf1213715294 12 13717956 3.70E-08 6.36E-07
vg1220408794 sf1220380236 12 20408794 5.88E-08 2.28E-06
vg1204324619 sf1204323607 12 4324619 5.52E-07 1.02E-06