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 mr1619 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
vg0406519287 sf0406514730 4 6519287 4.53E-19 7.27E-15
vg0406562314 sf0406557757 4 6562314 1.13E-18 7.53E-14
vg0406056747 sf0406052186 4 6056747 2.31E-09 3.89E-08
vg1208828240 sf1208825647 12 8828240 3.40E-09 1.46E-06
vg0521569979 sf0521507420 5 21569979 5.85E-09 6.82E-07
vg1017130098 sf1017058870 10 17130098 6.77E-09 4.85E-06
vg1122924753 sf1122458624 11 22924753 5.86E-08 1.19E-06
vg0124173863 sf0124172819 1 24173863 6.83E-08 1.46E-06
vg1003486707 sf1003485684 10 3486707 1.20E-07 2.59E-06
vg0202518756 sf0202518754 2 2518756 1.39E-07 4.58E-07
vg1209921454 sf1209918864 12 9921454 3.01E-07 9.41E-07
vg0807117547 sf0807116552 8 7117547 3.06E-07 2.32E-06