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 mr1122 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
vg0524430402 sf0524367823 5 24430402 4.08E-28 NA
vg0524496368 sf0524433789 5 24496368 6.28E-28 3.76E-06
vg0524468976 sf0524406397 5 24468976 6.30E-28 NA
vg0900894793 sf0900893793 9 894793 6.79E-27 NA
vg1113241003 sf1112777324 11 13241003 3.03E-26 NA
vg0105075602 sf0105074602 1 5075602 3.74E-26 NA
vg0207675934 sf0207675934 2 7675934 5.68E-26 NA
vg0208020311 sf0208020310 2 8020311 7.86E-22 8.82E-06
vg1126079756 sf1125608170 11 26079756 NA 2.18E-07
vg0900430619 sf0900429619 9 430619 NA 1.12E-06
vg0431958265 sf0431773160 4 31958265 NA 1.19E-06
vg0431983222 sf0431798115 4 31983222 NA 1.23E-06
vg0306633863 sf0306632863 3 6633863 NA 1.47E-06
vg0225316083 sf0225310214 2 25316083 NA 3.92E-06