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 mr1973 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
vg0607267655 sf0607266656 6 7267655 3.89E-50 5.67E-36
vg0607417912 sf0607416913 6 7417912 2.75E-18 2.85E-08
vg0429319504 sf0429134370 4 29319504 1.12E-15 NA
vg0607310239 sf0607309240 6 7310239 1.45E-15 5.47E-16
vg0908369319 sf0908368319 9 8369319 4.82E-15 NA
vg0607346885 sf0607345886 6 7346885 5.54E-15 1.60E-14
vg0805703765 sf0805702768 8 5703765 3.54E-14 NA
vg0607025048 sf0607024049 6 7025048 5.37E-14 1.16E-07
vg0224817842 sf0224811973 2 24817842 4.45E-13 4.67E-07
vg0334582408 sf0334575278 3 34582408 1.27E-12 3.06E-06
vg0619887922 sf0619886925 6 19887922 2.46E-12 1.84E-07
vg0623001816 sf0623000819 6 23001816 3.40E-12 1.22E-07
vg0102657456 sf0102656456 1 2657456 2.47E-10 2.97E-06
vg0123678952 sf0123677908 1 23678952 3.73E-09 2.82E-06
vg0607519601 sf0607518602 6 7519601 1.69E-08 1.21E-08
vg0131651142 sf0131650098 1 31651142 7.78E-08 2.97E-09
vg0312485967 sf0312484685 3 12485967 NA 2.56E-06
vg0206101334 sf0206101334 2 6101334 NA 2.72E-06
vg0136251646 sf0136250603 1 36251646 NA 4.09E-06
vg0904401262 sf0904400262 9 4401262 NA 4.44E-06
vg0136211264 sf0136210221 1 36211264 NA 4.98E-06