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 mr1474 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
vg0912264986 sf0912263985 9 12264986 3.27E-07 3.27E-07
vg1224938358 sf1224904812 12 24938358 3.57E-07 3.57E-07
vg0610793738 sf0610792739 6 10793738 3.79E-07 3.79E-07
vg1203437431 sf1203436430 12 3437431 8.66E-07 8.66E-07
vg0421459150 sf0421287201 4 21459150 1.56E-06 1.56E-06
vg1125860780 sf1125394699 11 25860780 1.78E-06 1.78E-06
vg0818047553 sf0818044840 8 18047553 3.07E-06 3.07E-06
vg0608084610 sf0608083611 6 8084610 3.12E-06 3.12E-06
vg0609173072 sf0609172073 6 9173072 4.62E-06 4.63E-06
vg1103306604 sf1103302507 11 3306604 4.79E-06 4.79E-06
vg0921393671 sf0921393190 9 21393671 9.17E-06 9.18E-06