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 mr1902 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
vg0724505923 sf0724504929 7 24505923 4.98E-28 1.59E-20
vg0331249174 sf0331242059 3 31249174 5.51E-28 5.97E-10
vg0724575067 sf0724574073 7 24575067 2.47E-27 1.56E-20
vg0331248975 sf0331241860 3 31248975 1.02E-26 2.77E-10
vg1115386291 sf1114922603 11 15386291 2.19E-17 NA
vg1111106567 sf1111100884 11 11106567 4.49E-17 NA
vg0137604571 sf0137603528 1 37604571 6.49E-16 NA
vg0724642298 sf0724641304 7 24642298 3.08E-14 3.91E-06
vg1119835197 sf1119369128 11 19835197 2.22E-13 NA
vg0331236124 sf0331229009 3 31236124 5.16E-13 8.39E-09
vg1011696221 sf1011625036 10 11696221 5.89E-13 8.20E-07
vg0225514496 sf0225508627 2 25514496 2.12E-12 NA
vg0325099885 sf0325097966 3 25099885 2.44E-12 2.53E-06
vg0136202716 sf0136201673 1 36202716 3.15E-11 NA
vg0724515347 sf0724514353 7 24515347 NA 6.34E-16
vg0724532089 sf0724531095 7 24532089 NA 3.29E-14
vg0724473205 sf0724472211 7 24473205 NA 2.96E-08
vg0507098360 sf0507098302 5 7098360 NA 8.72E-07
vg0410306276 sf0410296974 4 10306276 NA 1.01E-06
vg0724401667 sf0724400673 7 24401667 NA 1.13E-06
vg0724588597 sf0724587603 7 24588597 NA 1.39E-06
vg0724381738 sf0724380744 7 24381738 NA 1.56E-06
vg0107007872 sf0107006872 1 7007872 NA 1.66E-06
vg0721876471 sf0721875478 7 21876471 NA 2.02E-06
vg0724504126 sf0724503132 7 24504126 NA 2.21E-06
vg1017092925 sf1017021697 10 17092925 NA 2.36E-06
vg0722461551 sf0722460558 7 22461551 NA 3.25E-06
vg0725312603 sf0725311609 7 25312603 NA 3.37E-06