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 mr1275 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
vg1215548475 sf1215545772 12 15548475 3.02E-08 3.02E-08
vg1217863038 sf1217834472 12 17863038 8.95E-07 8.95E-07
vg1212214384 sf1212211722 12 12214384 1.72E-06 1.72E-06
vg1221694446 sf1221660993 12 21694446 1.74E-06 1.74E-06
vg1212597775 sf1212595114 12 12597775 2.45E-06 2.45E-06
vg1217682087 sf1217676042 12 17682087 2.89E-06 2.89E-06
vg1221621923 sf1221588470 12 21621923 3.45E-06 3.45E-06
vg0813446827 sf0813444380 8 13446827 4.86E-06 4.86E-06