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 mr1990 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
vg1217042210 sf1217036164 12 17042210 4.16E-11 3.41E-06
vg0919859957 sf0919859476 9 19859957 9.72E-10 NA
vg0421061649 sf0420889704 4 21061649 1.58E-09 4.65E-06
vg0701536585 sf0701535585 7 1536585 1.98E-09 NA
vg0809586152 sf0809585156 8 9586152 3.37E-09 1.35E-07
vg0324098753 sf0324096832 3 24098753 1.06E-08 NA
vg0213655666 sf0213655662 2 13655666 1.09E-08 1.55E-06
vg1216471043 sf1216468336 12 16471043 1.44E-08 7.02E-07
vg0504754700 sf0504754677 5 4754700 1.65E-07 NA