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 mr1442 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
vg1017098057 sf1017026829 10 17098057 5.22E-07 5.22E-07
vg1017232696 sf1017161469 10 17232696 1.17E-06 1.17E-06
vg1205810555 sf1205809537 12 5810555 2.14E-06 2.14E-06
vg1016458264 sf1016387037 10 16458264 2.42E-06 2.42E-06
vg0601448111 sf0601447112 6 1448111 2.90E-06 2.90E-06