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 mr1944 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
vg1215076732 sf1215074073 12 15076732 3.59E-09 5.82E-06
vg0920272507 sf0920272026 9 20272507 6.78E-09 2.51E-07
vg1213717963 sf1213715301 12 13717963 6.96E-09 3.37E-07
vg1102677343 sf1102673247 11 2677343 1.73E-08 1.91E-06
vg0706897364 sf0706896369 7 6897364 3.07E-08 1.37E-06
vg1115697103 sf1115233412 11 15697103 8.09E-08 NA
vg0403315819 sf0403311422 4 3315819 1.29E-07 3.83E-06