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 mr1051 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
vg0921537073 sf0921536592 9 21537073 2.54E-36 1.62E-12
vg0921465189 sf0921464708 9 21465189 7.13E-36 1.51E-12
vg0133703611 sf0133702567 1 33703611 2.37E-34 3.60E-07
vg0133599784 sf0133598740 1 33599784 4.83E-32 3.80E-11
vg0709326096 sf0709325102 7 9326096 1.51E-31 NA
vg0130714423 sf0130713379 1 30714423 9.75E-31 NA
vg0905150688 sf0905149688 9 5150688 1.05E-30 NA
vg0130956505 sf0130955461 1 30956505 8.12E-30 4.49E-06
vg1022503385 sf1022431859 10 22503385 7.01E-29 NA
vg0629714028 sf0629713030 6 29714028 4.90E-28 NA
vg0127430545 sf0127429501 1 27430545 4.10E-27 1.13E-06
vg0921540025 sf0921539544 9 21540025 NA 4.20E-14
vg0608564755 sf0608563756 6 8564755 NA 3.21E-07
vg0812039435 sf0812038440 8 12039435 NA 1.22E-06
vg1217056602 sf1217050557 12 17056602 NA 1.32E-06
vg0330463056 sf0330455945 3 30463056 NA 2.49E-06
vg1215216305 sf1215213602 12 15216305 NA 3.84E-06
vg0915747848 sf0915746847 9 15747848 NA 5.68E-06