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 mr1876 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
vg0808162481 sf0808161485 8 8162481 7.15E-08 8.28E-06
vg0315348932 sf0315347579 3 15348932 9.45E-08 NA
vg0320740955 sf0320739465 3 20740955 1.85E-06 NA
vg1218126488 sf1218097924 12 18126488 NA 1.02E-08
vg1119485334 sf1119019022 11 19485334 NA 6.21E-08
vg1119486675 sf1119020363 11 19486675 NA 1.07E-07
vg1110517362 sf1110511907 11 10517362 NA 3.11E-06
vg0407849294 sf0407844562 4 7849294 NA 7.29E-06