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 mr1443 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
vg1217491800 sf1217485755 12 17491800 1.61E-09 NA
vg0215631406 sf0215625536 2 15631406 2.11E-09 NA
vg0212876512 sf0212876508 2 12876512 3.82E-09 NA
vg0630767534 sf0630766536 6 30767534 7.44E-09 NA
vg0821334599 sf0821331886 8 21334599 8.08E-09 NA
vg0729442292 sf0729441300 7 29442292 2.16E-08 NA
vg1016616995 sf1016545768 10 16616995 1.18E-06 2.43E-06
vg1102804893 sf1102800797 11 2804893 NA 2.35E-06