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 mr1851 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
vg0419232304 sf0419060342 4 19232304 1.30E-13 9.45E-09
vg0419216517 sf0419044555 4 19216517 4.58E-13 4.35E-09
vg0804859344 sf0804858347 8 4859344 2.06E-09 6.23E-07
vg0804997889 sf0804996892 8 4997889 1.32E-08 NA
vg1218772233 sf1218743668 12 18772233 2.09E-08 NA
vg0811613659 sf0811612664 8 11613659 9.51E-08 NA
vg1004203611 sf1004134597 10 4203611 1.19E-07 3.10E-06
vg0806568875 sf0806567880 8 6568875 4.67E-07 2.34E-06