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 mr1627 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
vg0141973203 sf0141972160 1 41973203 2.14E-19 8.89E-06
vg0141770102 sf0141769059 1 41770102 2.88E-18 2.27E-06
vg0728156014 sf0728155021 7 28156014 3.11E-17 NA
vg0123684702 sf0123683658 1 23684702 5.80E-17 NA
vg0820850557 sf0820847844 8 20850557 3.39E-16 NA
vg1207667840 sf1207665244 12 7667840 1.17E-14 NA
vg0714622950 sf0714621957 7 14622950 2.32E-11 3.49E-08
vg0709448532 sf0709447538 7 9448532 8.81E-11 4.57E-06
vg0630515806 sf0630514808 6 30515806 1.52E-10 NA
vg0912189735 sf0912188734 9 12189735 1.89E-09 NA
vg0231991021 sf0231985152 2 31991021 2.21E-08 NA