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 mr1850 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
vg0610369842 sf0610368843 6 10369842 9.67E-29 5.35E-14
vg0612914787 sf0612913788 6 12914787 6.16E-19 NA
vg0617359224 sf0617358227 6 17359224 5.99E-17 NA
vg0629122299 sf0629121301 6 29122299 5.04E-14 NA
vg0610473706 sf0610472707 6 10473706 4.47E-13 3.27E-07
vg0612016547 sf0612015548 6 12016547 1.22E-12 3.88E-06
vg0610135032 sf0610134033 6 10135032 1.04E-11 2.53E-07
vg0610590324 sf0610589325 6 10590324 1.55E-11 1.14E-06
vg0610103727 sf0610102728 6 10103727 1.74E-11 9.42E-07
vg0610475122 sf0610474123 6 10475122 4.21E-11 2.67E-07
vg0610370420 sf0610369421 6 10370420 1.38E-08 5.29E-08
vg0614774949 sf0614773950 6 14774949 2.25E-08 3.37E-06
vg0113416401 sf0113415375 1 13416401 NA 2.47E-06
vg0103824970 sf0103823970 1 3824970 NA 4.52E-06