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 mr1647 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
vg0222337580 sf0222331711 2 22337580 4.81E-08 4.81E-08
vg0221843984 sf0221838115 2 21843984 2.17E-07 2.17E-07
vg0321576473 sf0321574983 3 21576473 2.41E-07 2.42E-07
vg0416930919 sf0416758961 4 16930919 3.23E-07 3.23E-07
vg0232543553 sf0232537684 2 32543553 9.31E-07 9.31E-07
vg0609832495 sf0609831496 6 9832495 1.49E-06 1.49E-06
vg0319113443 sf0319112203 3 19113443 1.90E-06 1.90E-06
vg0819431872 sf0819429159 8 19431872 2.08E-06 2.08E-06
vg0605572207 sf0605571208 6 5572207 2.26E-06 2.26E-06
vg0819150140 sf0819147427 8 19150140 2.51E-06 2.51E-06
vg0219780702 sf0219774834 2 19780702 2.85E-06 2.85E-06
vg0304938711 sf0304937713 3 4938711 2.89E-06 2.89E-06
vg1010572055 sf1010500876 10 10572055 2.96E-06 2.96E-06
vg1010888144 sf1010816964 10 10888144 2.99E-06 2.99E-06
vg0906975807 sf0906974807 9 6975807 3.17E-06 3.17E-06
vg1004685372 sf1004701909 10 4685372 3.32E-06 3.32E-06
vg0227578016 sf0227572147 2 27578016 3.78E-06 3.78E-06
vg0610852582 sf0610851583 6 10852582 4.42E-06 4.42E-06
vg0204233998 sf0204233995 2 4233998 4.46E-06 4.46E-06