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 mr1707 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
vg1124328383 sf1123862253 11 24328383 1.32E-08 NA
vg0706508455 sf0706507460 7 6508455 2.46E-08 4.86E-06
vg1006649418 sf1006665041 10 6649418 7.67E-08 NA
vg0601639995 sf0601638996 6 1639995 4.80E-07 2.41E-06
vg1004244571 sf1004261109 10 4244571 9.74E-06 NA