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 mr1916 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
vg0107047780 sf0107046780 1 7047780 2.23E-16 7.17E-08
vg0827125579 sf0827122865 8 27125579 1.69E-15 7.83E-07
vg0914907851 sf0914906850 9 14907851 1.01E-14 3.80E-06
vg0921699962 sf0921699481 9 21699962 1.86E-14 2.91E-06
vg0805970126 sf0805969129 8 5970126 2.07E-14 1.76E-06
vg1215096865 sf1215094202 12 15096865 2.28E-14 4.63E-06
vg0218104924 sf0218099055 2 18104924 5.26E-13 3.98E-06
vg0223262220 sf0223256351 2 23262220 1.57E-10 1.02E-06
vg0127040944 sf0127039900 1 27040944 9.18E-10 8.71E-07
vg0335284080 sf0335276949 3 35284080 NA 4.69E-07
vg0205347525 sf0205347525 2 5347525 NA 3.06E-06