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 mr1074 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
vg0222725881 sf0222720012 2 22725881 2.67E-60 3.76E-26
vg0723580060 sf0723579067 7 23580060 9.11E-32 NA
vg0626350572 sf0626349575 6 26350572 2.59E-31 NA
vg1203806115 sf1203805114 12 3806115 1.29E-30 NA
vg0214392322 sf0214386452 2 14392322 2.90E-30 NA
vg0130697648 sf0130696604 1 30697648 NA 1.19E-13
vg0222725003 sf0222719134 2 22725003 NA 4.47E-11
vg0223740729 sf0223734860 2 23740729 NA 5.09E-08
vg0130661668 sf0130660624 1 30661668 NA 3.01E-07
vg0222817468 sf0222811599 2 22817468 NA 4.88E-07
vg1203473350 sf1203472350 12 3473350 NA 1.84E-06