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 mr1397 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
vg1104448944 sf1104444846 11 4448944 2.60E-09 7.04E-08
vg1104448929 sf1104444831 11 4448929 3.27E-09 6.21E-08
vg0921004343 sf0921003862 9 21004343 1.08E-08 4.85E-08
vg0421016689 sf0420844742 4 21016689 3.49E-08 5.16E-06
vg0421030366 sf0420858419 4 21030366 5.42E-08 2.39E-06
vg0805826839 sf0805825842 8 5826839 9.27E-08 5.51E-07
vg1104467562 sf1104463464 11 4467562 1.27E-07 2.23E-06
vg0420798136 sf0420626179 4 20798136 1.62E-07 2.17E-07
vg0516508609 sf0516451091 5 16508609 1.67E-07 2.25E-07
vg1114618741 sf1114155059 11 14618741 1.85E-07 3.17E-07
vg0709448532 sf0709447538 7 9448532 6.49E-07 5.96E-07
vg0721076186 sf0721075193 7 21076186 9.57E-07 1.65E-06
vg0410295994 sf0410286692 4 10295994 3.52E-06 4.74E-06
vg1215307750 sf1215305048 12 15307750 5.23E-06 3.37E-06
vg0513235168 sf0513178090 5 13235168 8.45E-06 1.02E-06