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 mr1741 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
vg1214703763 sf1214701104 12 14703763 5.02E-09 NA
vg0709987989 sf0709986995 7 9987989 3.85E-08 NA
vg0428801373 sf0428616223 4 28801373 3.86E-08 NA
vg0618214950 sf0618213953 6 18214950 4.61E-08 NA
vg0710231860 sf0710230866 7 10231860 6.66E-08 NA
vg0432860646 sf0432675533 4 32860646 8.62E-08 4.61E-07
vg0207729665 sf0207729664 2 7729665 NA 2.28E-06