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 mr1521 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
vg0420295257 sf0420123302 4 20295257 5.90E-10 NA
vg0315008270 sf0315006917 3 15008270 7.84E-10 NA
vg0313641931 sf0313640648 3 13641931 1.02E-09 8.82E-06
vg0720634569 sf0720633576 7 20634569 1.41E-09 NA
vg0314967098 sf0314965745 3 14967098 4.18E-09 4.90E-06
vg0414202308 sf0414193024 4 14202308 5.84E-09 NA
vg1115168100 sf1114704414 11 15168100 6.20E-08 2.74E-06
vg1226283597 sf1226249991 12 26283597 3.65E-07 1.09E-06