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 mr1396 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
vg0211794496 sf0211794492 2 11794496 1.07E-06 1.07E-06
vg0518112505 sf0518051991 5 18112505 1.34E-06 1.35E-06
vg0507563644 sf0507563585 5 7563644 1.48E-06 1.48E-06
vg0522884888 sf0522822330 5 22884888 1.97E-06 1.97E-06
vg1117177660 sf1116711512 11 17177660 2.45E-06 2.45E-06
vg0502042542 sf0502042524 5 2042542 2.74E-06 2.74E-06
vg0220406103 sf0220400235 2 20406103 3.01E-06 3.01E-06
vg1123942722 sf1123476592 11 23942722 3.35E-06 3.36E-06
vg0308977626 sf0308976564 3 8977626 3.42E-06 3.42E-06
vg0401333600 sf0401329150 4 1333600 3.92E-06 3.92E-06
vg0119377829 sf0119376784 1 19377829 3.97E-06 3.96E-06
vg0411807088 sf0411797799 4 11807088 4.33E-06 4.34E-06