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 mr1590 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
vg1117789128 sf1117322984 11 17789128 2.90E-08 NA
vg0431811408 sf0431626301 4 31811408 4.91E-08 NA
vg0123795673 sf0123794629 1 23795673 5.01E-08 NA
vg0123784103 sf0123783059 1 23784103 5.75E-07 2.76E-06
vg0224592034 sf0224586165 2 24592034 1.16E-06 2.18E-06
vg0217864370 sf0217858501 2 17864370 1.19E-06 3.17E-06
vg1207248243 sf1207245650 12 7248243 1.68E-06 1.01E-06
vg0123436071 sf0123435027 1 23436071 8.12E-06 9.26E-07
vg0713683284 sf0713682291 7 13683284 8.53E-06 NA
vg0208608994 sf0208608993 2 8608994 NA 2.12E-06
vg1217896758 sf1217868192 12 17896758 NA 2.61E-06