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 mr1945 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
vg1125118463 sf1124652303 11 25118463 2.77E-27 2.77E-27
vg1124875808 sf1124409648 11 24875808 6.64E-10 6.64E-10
vg1124918104 sf1124451944 11 24918104 6.94E-10 6.94E-10
vg1124914537 sf1124448377 11 24914537 4.35E-09 4.35E-09
vg0106089280 sf0106088280 1 6089280 1.71E-07 1.71E-07
vg0224673331 sf0224667462 2 24673331 6.74E-07 6.73E-07
vg0614114557 sf0614113558 6 14114557 8.23E-07 8.23E-07
vg0814644598 sf0814641884 8 14644598 1.34E-06 1.34E-06
vg0208287795 sf0208287794 2 8287795 1.37E-06 1.37E-06
vg0408276746 sf0408272020 4 8276746 1.43E-06 1.43E-06
vg0301241360 sf0301240358 3 1241360 3.31E-06 3.31E-06
vg0328637867 sf0328630920 3 28637867 4.42E-06 4.42E-06