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 mr1953 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
vg1214822308 sf1214819649 12 14822308 4.67E-07 4.67E-07
vg0103381628 sf0103380628 1 3381628 9.61E-07 9.61E-07
vg1219593314 sf1219564784 12 19593314 2.67E-06 2.67E-06
vg0820865298 sf0820862585 8 20865298 2.70E-06 2.70E-06
vg0213822498 sf0213816628 2 13822498 4.02E-06 4.02E-06
vg0823477885 sf0823475172 8 23477885 4.60E-06 4.60E-06