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 mr1882 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
vg0819864501 sf0819861788 8 19864501 1.36E-41 5.83E-07
vg0802140056 sf0802139059 8 2140056 1.44E-41 5.94E-07
vg1116106871 sf1115641744 11 16106871 1.15E-40 NA
vg1119446199 sf1118979887 11 19446199 1.70E-40 NA
vg0607101713 sf0607100714 6 7101713 2.25E-40 NA
vg1223868448 sf1223834901 12 23868448 6.48E-40 3.15E-06
vg1219410791 sf1219382261 12 19410791 NA 2.29E-07
vg0306330280 sf0306329280 3 6330280 NA 1.30E-06
vg0221339299 sf0221333431 2 21339299 NA 1.58E-06
vg0132898168 sf0132897124 1 32898168 NA 2.20E-06
vg1210741341 sf1210738705 12 10741341 NA 2.42E-06
vg0234244837 sf0234238968 2 34244837 NA 2.83E-06