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 mr1199 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
vg0719093690 sf0719092697 7 19093690 5.25E-24 8.31E-08
vg0719209499 sf0719208506 7 19209499 7.67E-24 5.60E-08
vg0304916014 sf0304915016 3 4916014 1.26E-21 NA
vg0707583684 sf0707582689 7 7583684 2.17E-21 NA
vg0704631041 sf0704630042 7 4631041 5.03E-21 NA
vg1202102394 sf1202101392 12 2102394 6.37E-21 NA
vg0304931155 sf0304930157 3 4931155 9.49E-20 8.33E-07
vg0211745251 sf0211745247 2 11745251 1.43E-18 4.12E-06
vg0706461994 sf0706460999 7 6461994 NA 4.18E-06
vg0223558576 sf0223552707 2 23558576 NA 7.56E-06
vg0105761081 sf0105760081 1 5761081 NA 8.51E-06