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 mr1883 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
vg0124253318 sf0124252274 1 24253318 5.42E-15 NA
vg0704638070 sf0704637071 7 4638070 5.60E-15 NA
vg0420659191 sf0420487234 4 20659191 6.78E-15 NA
vg0305242441 sf0305241441 3 5242441 1.26E-14 NA
vg0813660047 sf0813657332 8 13660047 1.51E-14 NA
vg0423639987 sf0423454844 4 23639987 8.49E-14 NA
vg0317655545 sf0317654327 3 17655545 2.04E-11 7.61E-07
vg0420699382 sf0420527425 4 20699382 NA 1.34E-06
vg0420689698 sf0420517741 4 20689698 NA 2.14E-06
vg0812659623 sf0812657448 8 12659623 NA 2.32E-06
vg0216382648 sf0216376778 2 16382648 NA 3.39E-06