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 mr1145 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
vg0719133785 sf0719132792 7 19133785 3.17E-16 7.68E-11
vg0719007567 sf0719006574 7 19007567 7.51E-15 1.88E-10
vg0719011406 sf0719010413 7 19011406 1.55E-14 7.40E-11
vg0719133362 sf0719132369 7 19133362 7.73E-13 3.10E-09
vg1202414715 sf1202413716 12 2414715 2.08E-11 3.16E-06
vg0719140315 sf0719139322 7 19140315 7.60E-11 3.76E-07
vg1202102394 sf1202101392 12 2102394 1.40E-10 8.03E-08
vg0611422032 sf0611421033 6 11422032 3.48E-10 NA
vg0611538131 sf0611537132 6 11538131 4.76E-10 4.98E-06
vg0719078237 sf0719077244 7 19078237 NA 3.28E-09
vg0718985954 sf0718984961 7 18985954 NA 2.32E-07
vg0719153233 sf0719152240 7 19153233 NA 8.93E-07
vg0503840950 sf0503840927 5 3840950 NA 1.11E-06
vg0718998483 sf0718997490 7 18998483 NA 1.83E-06
vg0706750728 sf0706749733 7 6750728 NA 2.23E-06
vg0427044235 sf0426859108 4 27044235 NA 2.62E-06