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 mr1114 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
vg0421387824 sf0421215877 4 21387824 8.83E-18 2.41E-14
vg1001348300 sf1001347277 10 1348300 9.60E-14 4.01E-09
vg0727970899 sf0727969906 7 27970899 1.19E-13 1.85E-09
vg0336193973 sf0336186899 3 36193973 1.37E-13 1.67E-10
vg0504720198 sf0504720175 5 4720198 5.33E-13 8.29E-09
vg1117137503 sf1116671355 11 17137503 3.37E-12 1.60E-10
vg0308535729 sf0308534667 3 8535729 2.74E-11 2.02E-07
vg1126461419 sf1125989832 11 26461419 7.84E-11 2.12E-07
vg1016339056 sf1016267832 10 16339056 6.26E-10 3.86E-07
vg1201867679 sf1201866676 12 1867679 1.44E-09 2.80E-07
vg0819366916 sf0819364203 8 19366916 1.92E-09 1.09E-07
vg1204507349 sf1204506337 12 4507349 2.03E-09 4.76E-07
vg1002009944 sf1002008921 10 2009944 2.04E-09 1.13E-07
vg0224540597 sf0224534728 2 24540597 6.74E-09 3.88E-07
vg0628759426 sf0628758428 6 28759426 1.09E-08 5.98E-07
vg0139756098 sf0139755055 1 39756098 4.39E-08 8.08E-07
vg0219292377 sf0219286509 2 19292377 8.15E-08 6.41E-08
vg0819421680 sf0819418967 8 19421680 1.15E-07 1.59E-07
vg0714480545 sf0714479552 7 14480545 2.25E-07 7.73E-08
vg1208630676 sf1208628083 12 8630676 NA 4.97E-08