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 mr1646 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
vg0805900956 sf0805899959 8 5900956 6.94E-09 5.57E-07
vg0915815139 sf0915814138 9 15815139 1.12E-08 NA
vg0805095019 sf0805094022 8 5095019 1.28E-08 NA
vg0528836237 sf0528773592 5 28836237 2.92E-08 NA
vg0509233251 sf0509233180 5 9233251 2.00E-07 2.24E-07
vg0816086900 sf0816084186 8 16086900 2.19E-07 2.70E-06
vg0906841774 sf0906840774 9 6841774 2.79E-06 NA
vg0804904491 sf0804903494 8 4904491 4.48E-06 NA