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 mr1296 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
vg0125510468 sf0125509424 1 25510468 5.88E-10 NA
vg0726932441 sf0726931447 7 26932441 1.75E-09 NA
vg0139783995 sf0139782952 1 39783995 3.78E-09 NA
vg0130844222 sf0130843178 1 30844222 5.70E-09 NA
vg0527926746 sf0527864103 5 27926746 6.09E-09 NA
vg1208054501 sf1208051907 12 8054501 1.52E-08 4.52E-06
vg0124205775 sf0124204731 1 24205775 6.46E-08 3.65E-06
vg0528836055 sf0528773410 5 28836055 1.59E-07 4.63E-06
vg0100854927 sf0100853927 1 854927 1.88E-07 NA
vg0800560523 sf0800559523 8 560523 2.76E-07 3.64E-06
vg0709128655 sf0709127661 7 9128655 2.33E-06 1.51E-06
vg0232481675 sf0232475806 2 32481675 3.08E-06 NA
vg0316491917 sf0316490562 3 16491917 3.77E-06 1.85E-06
vg0709322762 sf0709321768 7 9322762 NA 2.52E-06
vg0409861930 sf0409852628 4 9861930 NA 2.69E-06