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 mr1345 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
vg1102677343 sf1102673247 11 2677343 8.83E-08 8.83E-08
vg0223262220 sf0223256351 2 23262220 3.62E-07 3.62E-07
vg1215059931 sf1215057273 12 15059931 8.17E-07 8.17E-07
vg0921699962 sf0921699481 9 21699962 8.42E-07 8.42E-07
vg1019872900 sf1019801400 10 19872900 2.63E-06 2.63E-06
vg0312773945 sf0312772663 3 12773945 2.88E-06 2.88E-06
vg0706209943 sf0706208944 7 6209943 3.52E-06 3.52E-06
vg1204111654 sf1204110642 12 4111654 3.54E-06 3.54E-06
vg1115141729 sf1114678043 11 15141729 3.90E-06 3.90E-06