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 mr1709 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
vg1003496760 sf1003495737 10 3496760 7.10E-69 3.07E-42
vg1003462874 sf1003461851 10 3462874 8.85E-66 9.95E-42
vg1003521569 sf1003520546 10 3521569 5.27E-61 2.40E-56
vg1003465379 sf1003464356 10 3465379 2.53E-52 3.18E-45
vg1003446689 sf1003445666 10 3446689 7.39E-48 3.62E-45
vg1003087335 sf1003086312 10 3087335 4.49E-38 4.21E-28
vg1003090865 sf1003089842 10 3090865 3.45E-32 9.21E-29
vg1003095982 sf1003094959 10 3095982 1.59E-26 2.43E-13
vg0717726887 sf0717725894 7 17726887 2.85E-26 5.13E-20
vg1209942861 sf1209940271 12 9942861 4.99E-24 9.25E-16
vg1003097804 sf1003096781 10 3097804 1.78E-22 8.73E-17
vg0515848995 sf0515791536 5 15848995 3.46E-22 7.50E-13
vg1215306171 sf1215303469 12 15306171 4.25E-21 2.40E-10
vg1003520346 sf1003519323 10 3520346 1.72E-20 4.56E-16
vg0909393050 sf0909392049 9 9393050 3.72E-17 8.42E-09
vg1003603685 sf1003602662 10 3603685 1.03E-16 8.26E-09
vg0422509978 sf0422324865 4 22509978 6.11E-15 9.58E-12
vg0515848994 sf0515791535 5 15848994 1.29E-14 2.71E-10
vg0211784502 sf0211784498 2 11784502 3.69E-14 3.29E-08
vg1003336967 sf1003335944 10 3336967 1.39E-13 7.79E-15
vg0210060826 sf0210060824 2 10060826 3.16E-13 1.91E-08
vg0623387556 sf0623386559 6 23387556 1.03E-12 9.50E-11
vg1003521634 sf1003520611 10 3521634 1.34E-08 1.20E-08
vg1003026779 sf1003025756 10 3026779 NA 5.32E-11