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 mr1795 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
vg0406401975 sf0406397415 4 6401975 3.66E-106 1.02E-13
vg0406535527 sf0406530970 4 6535527 4.30E-103 5.18E-14
vg0406465683 sf0406461126 4 6465683 1.57E-101 7.11E-15
vg0304913055 sf0304912057 3 4913055 2.46E-97 NA
vg0706510507 sf0706509512 7 6510507 2.24E-95 NA
vg0626799127 sf0626798130 6 26799127 4.28E-95 NA
vg0917998644 sf0917997643 9 17998644 8.31E-94 NA
vg0817436608 sf0817433894 8 17436608 4.27E-89 3.57E-07
vg0222719698 sf0222713829 2 22719698 NA 6.10E-15
vg0222743387 sf0222737518 2 22743387 NA 2.63E-11
vg0223172226 sf0223166357 2 23172226 NA 3.23E-07
vg0406521772 sf0406517215 4 6521772 NA 7.20E-07
vg1010292912 sf1010221733 10 10292912 NA 1.04E-06
vg0601656131 sf0601655132 6 1656131 NA 1.34E-06
vg1209897018 sf1209894428 12 9897018 NA 2.16E-06
vg0224620639 sf0224614770 2 24620639 NA 2.70E-06
vg1011932223 sf1011861038 10 11932223 NA 3.30E-06
vg0626294821 sf0626293824 6 26294821 NA 3.91E-06
vg0224702963 sf0224697094 2 24702963 NA 4.40E-06
vg0406523938 sf0406519381 4 6523938 NA 4.59E-06