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 mr1103 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
vg0719055987 sf0719054994 7 19055987 3.28E-16 4.13E-17
vg0719040385 sf0719039392 7 19040385 1.29E-15 3.20E-17
vg0719056561 sf0719055568 7 19056561 1.36E-14 7.96E-17
vg0719067465 sf0719066472 7 19067465 9.17E-12 3.75E-11
vg0719125702 sf0719124709 7 19125702 3.65E-11 2.77E-11
vg1101991503 sf1101987361 11 1991503 1.44E-08 7.46E-08
vg0107198487 sf0107197487 1 7198487 5.77E-08 5.08E-06
vg0228933475 sf0228927606 2 28933475 6.27E-08 4.45E-06
vg0516162890 sf0516105374 5 16162890 4.47E-07 2.51E-06
vg0421592157 sf0421420207 4 21592157 NA 2.13E-06