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 mr1050 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
vg0424050531 sf0423865392 4 24050531 1.03E-11 NA
vg0330783468 sf0330776355 3 30783468 1.52E-11 9.13E-07
vg0330740490 sf0330733377 3 30740490 2.02E-11 3.91E-07
vg0714507911 sf0714506918 7 14507911 1.08E-09 NA
vg1102427650 sf1102423554 11 2427650 1.38E-09 NA
vg0427531252 sf0427346113 4 27531252 4.78E-09 NA
vg0826398386 sf0826395672 8 26398386 5.12E-07 NA