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 mr1180 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
vg0222735698 sf0222729829 2 22735698 2.10E-24 4.48E-26
vg0222725003 sf0222719134 2 22725003 2.01E-22 1.03E-09
vg0131785830 sf0131784786 1 31785830 3.37E-19 NA
vg0222716080 sf0222710211 2 22716080 8.28E-18 3.23E-07
vg0504703202 sf0504703179 5 4703202 7.62E-17 NA
vg0506183773 sf0506183712 5 6183773 7.45E-15 NA
vg0818684028 sf0818681315 8 18684028 2.08E-11 NA
vg0222732658 sf0222726789 2 22732658 3.36E-11 4.82E-11
vg0907140746 sf0907139746 9 7140746 1.09E-10 NA
vg0224676560 sf0224670691 2 24676560 1.69E-10 6.06E-07
vg0223740729 sf0223734860 2 23740729 2.82E-10 1.90E-08
vg0110176224 sf0110175200 1 10176224 NA 3.43E-08
vg0222628695 sf0222622826 2 22628695 NA 1.34E-07
vg1215653812 sf1215651109 12 15653812 NA 6.40E-07
vg0622958104 sf0622957107 6 22958104 NA 7.79E-07
vg0224221184 sf0224215315 2 24221184 NA 1.29E-06
vg1007381584 sf1007397207 10 7381584 NA 1.80E-06
vg0224480548 sf0224474679 2 24480548 NA 1.90E-06
vg0410675332 sf0410666032 4 10675332 NA 3.76E-06
vg0501156158 sf0501156142 5 1156158 NA 4.69E-06
vg0317032441 sf0317031315 3 17032441 NA 4.72E-06