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 mr1726 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
vg0601625010 sf0601624011 6 1625010 1.11E-20 4.31E-06
vg0405675812 sf0405671251 4 5675812 5.66E-19 NA
vg1111696800 sf1111691117 11 11696800 6.04E-19 NA
vg0100617428 sf0100616428 1 617428 7.87E-18 NA
vg0919811919 sf0919811438 9 19811919 1.50E-17 NA
vg0405364448 sf0405359889 4 5364448 7.00E-17 1.40E-06
vg0620203384 sf0620202387 6 20203384 3.36E-16 2.17E-06
vg1020708879 sf1020637358 10 20708879 3.67E-16 1.67E-07
vg0420830788 sf0420658831 4 20830788 NA 7.03E-07
vg0420830827 sf0420658870 4 20830827 NA 8.25E-07
vg0506743734 sf0506743676 5 6743734 NA 4.39E-06