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 mr1547 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
vg1003403367 sf1003402344 10 3403367 4.61E-26 1.97E-19
vg1003401204 sf1003400181 10 3401204 4.68E-26 7.86E-20
vg1215306171 sf1215303469 12 15306171 1.33E-12 7.99E-09
vg1003133816 sf1003132793 10 3133816 1.33E-11 4.71E-10
vg0717726887 sf0717725894 7 17726887 1.40E-10 6.35E-08
vg0422509978 sf0422324865 4 22509978 1.76E-10 9.90E-09
vg1209942861 sf1209940271 12 9942861 2.31E-10 5.04E-07
vg0717601450 sf0717600457 7 17601450 3.43E-10 1.45E-09
vg0211784502 sf0211784498 2 11784502 6.46E-09 1.61E-06
vg0623387556 sf0623386559 6 23387556 1.51E-07 3.55E-06
vg0611197335 sf0611196336 6 11197335 2.18E-07 4.88E-08
vg0709339725 sf0709338731 7 9339725 4.30E-06 2.44E-06
vg1109260988 sf1109255565 11 9260988 6.65E-06 NA