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 mr1659 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
vg1217943070 sf1217914504 12 17943070 4.05E-07 4.05E-07
vg0809156316 sf0809155320 8 9156316 6.04E-07 6.04E-07
vg0820072079 sf0820069366 8 20072079 6.45E-07 6.45E-07
vg0112036166 sf0112035140 1 12036166 6.52E-07 6.52E-07
vg0821623988 sf0821621275 8 21623988 1.84E-06 1.84E-06
vg0815900368 sf0815897654 8 15900368 2.54E-06 2.54E-06
vg1215548475 sf1215545772 12 15548475 2.56E-06 2.57E-06