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 mr1877 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
vg0610648813 sf0610647814 6 10648813 2.41E-08 2.41E-08
vg1214762481 sf1214759822 12 14762481 1.97E-07 1.97E-07
vg0307407699 sf0307406631 3 7407699 4.80E-07 4.80E-07
vg0717377650 sf0717376657 7 17377650 8.91E-07 8.91E-07
vg1117924359 sf1117458217 11 17924359 1.19E-06 1.19E-06
vg0710253991 sf0710252997 7 10253991 3.21E-06 3.21E-06
vg0124037134 sf0124036090 1 24037134 3.95E-06 3.95E-06
vg0429608547 sf0429423415 4 29608547 4.01E-06 4.01E-06
vg0307814706 sf0307813644 3 7814706 4.55E-06 4.56E-06