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 mr1077 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
vg0623955389 sf0623954392 6 23955389 1.91E-10 NA
vg1216567539 sf1216564832 12 16567539 5.93E-10 NA
vg0426619931 sf0426434804 4 26619931 6.45E-10 NA
vg0432673364 sf0432488253 4 32673364 6.47E-10 NA
vg0324965295 sf0324963375 3 24965295 7.13E-10 9.85E-06
vg0316346281 sf0316344928 3 16346281 1.02E-09 3.63E-06
vg0810822568 sf0810821573 8 10822568 7.77E-09 1.59E-06
vg0722240976 sf0722239983 7 22240976 1.86E-08 NA
vg0432879824 sf0432694711 4 32879824 2.90E-08 NA
vg0228174656 sf0228168787 2 28174656 1.29E-06 NA
vg0326694691 sf0326687745 3 26694691 1.65E-06 NA
vg1004919122 sf1004935659 10 4919122 NA 5.18E-06