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 mr1205 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
vg1001300112 sf1001299089 10 1300112 1.05E-08 5.71E-06
vg0424939176 sf0424754037 4 24939176 4.88E-08 NA
vg0113990076 sf0113989050 1 13990076 5.47E-08 NA
vg0402123330 sf0402118924 4 2123330 6.41E-08 NA
vg0118124341 sf0118123295 1 18124341 9.29E-08 NA
vg1125009665 sf1124543505 11 25009665 3.38E-07 NA
vg0119596620 sf0119595575 1 19596620 1.02E-06 NA
vg0103256578 sf0103255578 1 3256578 5.37E-06 NA