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 mr1191 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
vg1127402538 sf1126930925 11 27402538 2.09E-17 2.09E-17
vg1127413986 sf1126942373 11 27413986 6.37E-12 6.37E-12
vg1127741204 sf1127269590 11 27741204 1.25E-11 1.25E-11
vg1125841143 sf1125375062 11 25841143 1.88E-10 1.88E-10
vg1125603546 sf1125137385 11 25603546 1.71E-09 1.71E-09
vg1208680127 sf1208677534 12 8680127 2.17E-09 2.17E-09
vg1127388655 sf1126917042 11 27388655 2.26E-09 2.26E-09
vg1109708668 sf1109703245 11 9708668 2.73E-09 2.73E-09
vg1125954146 sf1125482560 11 25954146 4.37E-09 4.37E-09
vg0807538911 sf0807537916 8 7538911 7.45E-09 7.45E-09
vg0619266995 sf0619265998 6 19266995 1.36E-08 1.36E-08
vg1106434198 sf1106429950 11 6434198 2.19E-08 2.19E-08
vg1220351136 sf1220322578 12 20351136 4.69E-08 4.69E-08
vg1125545040 sf1125078879 11 25545040 4.97E-08 4.97E-08
vg0421657372 sf0421485422 4 21657372 8.01E-08 8.01E-08
vg1127480962 sf1127009349 11 27480962 8.39E-08 8.39E-08
vg0104833420 sf0104832420 1 4833420 1.16E-07 1.16E-07
vg0207385548 sf0207385548 2 7385548 1.19E-07 1.19E-07
vg0429172806 sf0428987668 4 29172806 1.46E-07 1.46E-07
vg1125874639 sf1125408558 11 25874639 1.80E-07 1.80E-07