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 mr1268 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
vg0133276668 sf0133275624 1 33276668 8.38E-16 2.47E-06
vg0139829401 sf0139828358 1 39829401 4.19E-12 NA
vg0133673919 sf0133672875 1 33673919 2.14E-11 8.80E-07
vg0133604167 sf0133603123 1 33604167 4.28E-11 NA
vg0123686506 sf0123685462 1 23686506 2.60E-10 NA
vg1224028084 sf1223994537 12 24028084 1.13E-09 NA
vg0133278115 sf0133277071 1 33278115 1.45E-09 9.37E-07
vg0128988129 sf0128987084 1 28988129 3.16E-06 NA