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 mr1051 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
vg0133208220 sf0133207176 1 33208220 9.25E-30 1.21E-11
vg0702530647 sf0702529648 7 2530647 2.41E-26 NA
vg0710290299 sf0710289305 7 10290299 3.89E-26 NA
vg0800860314 sf0800859316 8 860314 5.83E-26 NA
vg0921465189 sf0921464708 9 21465189 8.39E-26 2.22E-06
vg0717363121 sf0717362128 7 17363121 1.25E-25 4.51E-06
vg0921431410 sf0921430929 9 21431410 2.71E-23 9.09E-08
vg0921543752 sf0921543271 9 21543752 NA 5.20E-10
vg0921420005 sf0921419524 9 21420005 NA 5.62E-10
vg1218299493 sf1218270929 12 18299493 NA 1.85E-07
vg0328947425 sf0328940477 3 28947425 NA 2.65E-07
vg1215955979 sf1215953275 12 15955979 NA 5.24E-07
vg0215099729 sf0215093859 2 15099729 NA 7.97E-07
vg1216261222 sf1216258518 12 16261222 NA 1.26E-06
vg0328922349 sf0328915401 3 28922349 NA 3.07E-06
vg0217657789 sf0217651919 2 17657789 NA 3.17E-06
vg1215218812 sf1215216109 12 15218812 NA 3.35E-06
vg1013060158 sf1012988973 10 13060158 NA 4.37E-06
vg1105411517 sf1105407268 11 5411517 NA 8.17E-06