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 mr1723 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
vg0333173989 sf0333166859 3 33173989 3.36E-29 3.11E-22
vg0333191872 sf0333184742 3 33191872 1.21E-28 9.68E-24
vg0333207813 sf0333200683 3 33207813 1.86E-13 2.71E-10
vg0333199277 sf0333192147 3 33199277 2.07E-13 2.55E-10
vg0332502161 sf0332495034 3 32502161 4.00E-13 7.96E-08
vg0332500781 sf0332493654 3 32500781 5.50E-13 8.73E-09
vg0700664294 sf0700663294 7 664294 7.62E-12 3.48E-07
vg0405048401 sf0405043840 4 5048401 7.99E-11 NA
vg0333484761 sf0333477631 3 33484761 2.08E-10 8.12E-08
vg0332944170 sf0332937040 3 32944170 2.33E-10 1.94E-06
vg0333266499 sf0333259369 3 33266499 6.34E-10 8.50E-09
vg0333155926 sf0333148796 3 33155926 1.35E-08 1.95E-06
vg1109703916 sf1109698493 11 9703916 1.55E-08 2.55E-06
vg0720951988 sf0720950995 7 20951988 3.06E-06 3.56E-06
vg0122065864 sf0122064819 1 22065864 NA 2.53E-06