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 mr1581 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
vg1020868172 sf1020796651 10 20868172 4.90E-23 4.07E-07
vg0708099149 sf0708098154 7 8099149 1.87E-22 6.12E-06
vg0115643513 sf0115642487 1 15643513 1.06E-21 NA
vg1218284485 sf1218255921 12 18284485 2.60E-21 NA
vg0419773387 sf0419601423 4 19773387 2.60E-21 NA
vg0210234945 sf0210234943 2 10234945 4.47E-19 4.92E-06
vg1219590404 sf1219561874 12 19590404 NA 6.66E-07
vg0311304375 sf0311303093 3 11304375 NA 9.07E-07
vg1125256284 sf1124790124 11 25256284 NA 1.74E-06
vg0817588459 sf0817585746 8 17588459 NA 1.85E-06
vg0528097115 sf0528034470 5 28097115 NA 2.59E-06
vg0528097069 sf0528034424 5 28097069 NA 4.21E-06
vg1115198301 sf1114734615 11 15198301 NA 4.57E-06