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 mr1682 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
vg0709448532 sf0709447538 7 9448532 2.19E-09 7.95E-08
vg1209814813 sf1209812223 12 9814813 6.39E-09 NA
vg0527361614 sf0527298970 5 27361614 6.78E-09 NA
vg1210833632 sf1210830998 12 10833632 1.13E-08 NA
vg1118347087 sf1117880945 11 18347087 3.23E-08 NA
vg0712843936 sf0712842943 7 12843936 8.15E-08 3.73E-06
vg1209756836 sf1209754246 12 9756836 8.57E-08 NA
vg0717352217 sf0717351224 7 17352217 8.90E-08 3.65E-06
vg1210750430 sf1210747794 12 10750430 1.95E-06 NA
vg0709235829 sf0709234835 7 9235829 6.14E-06 NA