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 mr1378 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
vg0141767249 sf0141766206 1 41767249 3.14E-13 NA
vg0123708170 sf0123707126 1 23708170 4.93E-13 NA
vg0726949721 sf0726948727 7 26949721 9.90E-13 NA
vg0138432101 sf0138431058 1 38432101 2.46E-11 NA
vg1217403986 sf1217397941 12 17403986 5.82E-11 NA
vg0704714916 sf0704713917 7 4714916 1.31E-09 3.65E-06
vg0920973553 sf0920973072 9 20973553 2.65E-09 5.92E-06
vg0307767570 sf0307766508 3 7767570 5.02E-09 3.10E-06
vg0100752622 sf0100751622 1 752622 6.22E-09 NA
vg0717367275 sf0717366282 7 17367275 2.07E-07 2.92E-07
vg0713247684 sf0713246691 7 13247684 7.50E-07 2.88E-07