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 mr1060 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
vg1022540722 sf1022469196 10 22540722 1.09E-09 2.85E-07
vg0906975807 sf0906974807 9 6975807 4.90E-09 9.88E-08
vg1226324348 sf1226290742 12 26324348 1.02E-08 8.11E-08
vg0328780990 sf0328774044 3 28780990 3.67E-08 2.03E-06
vg0520406859 sf0520344331 5 20406859 1.06E-07 3.00E-06
vg0716168165 sf0716167172 7 16168165 1.88E-07 3.84E-06
vg1010710062 sf1010638883 10 10710062 7.80E-07 1.70E-06
vg1022753746 sf1022682220 10 22753746 1.46E-06 5.74E-06
vg1222749071 sf1222715510 12 22749071 NA 4.89E-06