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 mr1503 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
vg0910844273 sf0910843272 9 10844273 4.12E-14 NA
vg0813557256 sf0813554809 8 13557256 8.50E-12 NA
vg0703851630 sf0703850631 7 3851630 2.53E-10 NA
vg0306755101 sf0306754101 3 6755101 4.19E-10 NA
vg0919021545 sf0919020545 9 19021545 9.24E-10 NA
vg0910867315 sf0910866314 9 10867315 1.19E-08 NA
vg0315944105 sf0315942752 3 15944105 1.45E-08 NA
vg0106102408 sf0106101408 1 6102408 9.07E-07 NA
vg0719016102 sf0719015109 7 19016102 1.73E-06 7.34E-06
vg0218459282 sf0218453413 2 18459282 5.22E-06 NA