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 mr1022 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
vg1215955191 sf1215952487 12 15955191 9.80E-27 1.50E-15
vg1014467198 sf1014395964 10 14467198 5.08E-11 NA
vg1213297058 sf1213294396 12 13297058 5.99E-11 NA
vg1204075471 sf1204074459 12 4075471 6.31E-11 NA
vg1018571610 sf1018500167 10 18571610 1.22E-10 NA
vg0702433302 sf0702432303 7 2433302 8.71E-10 3.17E-06
vg1215978141 sf1215975437 12 15978141 NA 3.57E-07
vg1215211990 sf1215209287 12 15211990 NA 7.26E-07
vg1215970005 sf1215967301 12 15970005 NA 8.91E-07
vg0610620315 sf0610619316 6 10620315 NA 4.06E-06
vg1216931811 sf1216925765 12 16931811 NA 4.14E-06