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 mr1571 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
vg0820890612 sf0820887899 8 20890612 1.31E-38 NA
vg0820872709 sf0820869996 8 20872709 1.37E-38 2.31E-06
vg0305892784 sf0305891784 3 5892784 2.47E-37 NA
vg0135571255 sf0135570212 1 35571255 2.65E-37 5.22E-06
vg0802264279 sf0802263282 8 2264279 6.79E-37 NA
vg0607315411 sf0607314412 6 7315411 9.63E-37 NA
vg0609861468 sf0609860469 6 9861468 NA 1.53E-14
vg0609872702 sf0609871703 6 9872702 NA 1.51E-10
vg0609830369 sf0609829370 6 9830369 NA 6.78E-10
vg0610435245 sf0610434246 6 10435245 NA 5.17E-09
vg0610069455 sf0610068456 6 10069455 NA 1.37E-07
vg0609888982 sf0609887983 6 9888982 NA 3.82E-07
vg0610553238 sf0610552239 6 10553238 NA 1.78E-06
vg1216723758 sf1216717712 12 16723758 NA 2.39E-06
vg0610323185 sf0610322186 6 10323185 NA 2.41E-06
vg1212822297 sf1212819636 12 12822297 NA 3.23E-06
vg0225134433 sf0225128564 2 25134433 NA 4.67E-06