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 mr1875 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
vg0122443930 sf0122442885 1 22443930 2.51E-11 1.73E-06
vg0727498088 sf0727497094 7 27498088 2.23E-08 NA
vg1117181891 sf1116715743 11 17181891 3.76E-08 NA
vg0309056044 sf0309054980 3 9056044 5.22E-08 NA
vg0123676253 sf0123675209 1 23676253 9.53E-08 NA
vg0612924201 sf0612923202 6 12924201 8.79E-07 NA
vg0706282472 sf0706281475 7 6282472 3.41E-06 NA
vg0727324847 sf0727323853 7 27324847 5.78E-06 2.40E-06
vg0712096394 sf0712095400 7 12096394 5.99E-06 NA
vg0122441794 sf0122440749 1 22441794 NA 5.22E-07
vg1226056282 sf1226022676 12 26056282 NA 7.18E-07
vg0916036241 sf0916035240 9 16036241 NA 4.94E-06