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 mr1239 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
vg0229845460 sf0229839591 2 29845460 9.96E-23 7.21E-06
vg0233282809 sf0233276940 2 33282809 5.44E-22 NA
vg1219627024 sf1219598494 12 19627024 6.16E-22 NA
vg0916109112 sf0916108111 9 16109112 8.76E-22 NA
vg0222725824 sf0222719955 2 22725824 1.01E-21 1.18E-06
vg0222725941 sf0222720072 2 22725941 1.13E-21 8.51E-07
vg1221620847 sf1221587394 12 21620847 9.05E-21 6.13E-06
vg0921539163 sf0921538682 9 21539163 NA 4.88E-06