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 mr1265 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
vg0716362688 sf0716361695 7 16362688 2.10E-11 1.72E-10
vg0139807697 sf0139806654 1 39807697 4.51E-11 NA
vg0716061853 sf0716060860 7 16061853 1.01E-10 1.67E-10
vg1102375085 sf1102370944 11 2375085 1.04E-10 NA
vg0827752431 sf0827749717 8 27752431 1.27E-09 NA
vg0717054416 sf0717053423 7 17054416 1.35E-09 5.24E-08
vg0717056384 sf0717055391 7 17056384 3.85E-09 1.34E-06
vg0716269579 sf0716268586 7 16269579 6.14E-08 1.43E-07
vg0716928357 sf0716927364 7 16928357 1.48E-07 1.99E-06
vg0432143982 sf0431958873 4 32143982 1.54E-07 1.35E-06
vg0432077668 sf0431892560 4 32077668 1.97E-07 7.73E-07
vg1117490256 sf1117024111 11 17490256 2.47E-07 1.35E-06
vg0717850162 sf0717849169 7 17850162 3.50E-07 2.59E-07
vg0805949886 sf0805948889 8 5949886 5.03E-07 5.26E-07
vg0123708079 sf0123707035 1 23708079 5.84E-07 NA
vg0306928785 sf0306927783 3 6928785 1.40E-06 3.41E-06
vg0421456445 sf0421284496 4 21456445 1.90E-06 1.60E-06
vg0110181846 sf0110180822 1 10181846 NA 3.85E-06
vg0517199790 sf0517139431 5 17199790 NA 3.97E-06