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 mr1557 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
vg0918924718 sf0918923718 9 18924718 2.32E-25 5.94E-15
vg0918922771 sf0918921771 9 18922771 3.73E-25 2.19E-15
vg0919489518 sf0919489108 9 19489518 2.79E-15 8.31E-06
vg0401207127 sf0401202677 4 1207127 1.06E-13 NA
vg0200466747 sf0200466747 2 466747 4.07E-13 NA
vg1123404382 sf1122938252 11 23404382 4.45E-13 NA
vg0919230563 sf0919230153 9 19230563 2.46E-11 3.71E-06
vg0119838948 sf0119837903 1 19838948 1.03E-09 NA
vg1104310512 sf1104306414 11 4310512 1.84E-09 NA
vg0918391108 sf0918390107 9 18391108 2.33E-09 5.34E-07
vg1202109317 sf1202108315 12 2109317 5.50E-08 NA
vg0918591039 sf0918590038 9 18591039 NA 1.75E-07
vg0224707683 sf0224701814 2 24707683 NA 3.42E-06