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 mr1109 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
vg0807727511 sf0807726516 8 7727511 2.44E-08 2.59E-07
vg0502297050 sf0502297025 5 2297050 2.84E-08 3.69E-06
vg0418797097 sf0418625142 4 18797097 9.33E-08 8.82E-07
vg0810407609 sf0810406613 8 10407609 1.12E-07 1.58E-06
vg0216763637 sf0216757767 2 16763637 5.16E-07 8.55E-07
vg0502167695 sf0502167670 5 2167695 6.82E-07 1.69E-06
vg0217134074 sf0217128204 2 17134074 3.34E-06 NA
vg0502283394 sf0502283369 5 2283394 3.69E-06 3.83E-06
vg0505749457 sf0505749395 5 5749457 8.44E-06 6.68E-06
vg0809578434 sf0809577438 8 9578434 8.92E-06 1.68E-06