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 mr1446 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
vg1012833649 sf1012762464 10 12833649 1.94E-12 4.73E-09
vg0709322599 sf0709321605 7 9322599 2.60E-09 5.29E-06
vg1222486091 sf1222452530 12 22486091 5.04E-09 3.58E-06
vg0327968455 sf0327961509 3 27968455 1.99E-08 3.17E-06
vg0133857992 sf0133856948 1 33857992 3.15E-08 NA
vg1222487174 sf1222453613 12 22487174 6.65E-08 4.48E-07
vg1211153360 sf1211150724 12 11153360 1.74E-06 NA
vg0912054345 sf0912053344 9 12054345 2.84E-06 1.40E-06
vg0720282120 sf0720281127 7 20282120 3.61E-06 NA