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 mr1150 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
vg0222729090 sf0222723221 2 22729090 2.55E-39 9.01E-32
vg0223077967 sf0223072098 2 23077967 1.15E-13 3.75E-08
vg0223077821 sf0223071952 2 23077821 1.80E-13 1.72E-08
vg0221693727 sf0221687858 2 21693727 1.10E-12 6.09E-07
vg0224529876 sf0224524007 2 24529876 1.51E-12 1.17E-07
vg0221658331 sf0221652462 2 21658331 1.93E-12 1.46E-07
vg0224876386 sf0224870517 2 24876386 1.57E-11 3.18E-07
vg0222765370 sf0222759501 2 22765370 2.69E-11 1.16E-07
vg0222634177 sf0222628308 2 22634177 5.82E-11 1.30E-07
vg0222799385 sf0222793516 2 22799385 6.72E-09 6.92E-09
vg0222729132 sf0222723263 2 22729132 7.75E-08 4.95E-06
vg0222624829 sf0222618960 2 22624829 1.08E-07 2.17E-06
vg0611557848 sf0611556849 6 11557848 2.14E-07 NA
vg0222679458 sf0222673589 2 22679458 1.30E-06 1.36E-06
vg0224832469 sf0224826600 2 24832469 NA 2.10E-06
vg0222525776 sf0222519907 2 22525776 NA 2.66E-06