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 mr1311 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
vg0420711795 sf0420539838 4 20711795 2.03E-08 2.03E-08
vg0805826839 sf0805825842 8 5826839 1.15E-07 1.15E-07
vg0921004343 sf0921003862 9 21004343 2.31E-07 2.31E-07
vg0424181194 sf0423996055 4 24181194 4.13E-07 4.13E-07
vg0421384856 sf0421212909 4 21384856 5.38E-07 5.38E-07
vg0706405260 sf0706404265 7 6405260 7.02E-07 7.03E-07
vg0516508609 sf0516451091 5 16508609 7.79E-07 7.79E-07
vg0801344289 sf0801343291 8 1344289 8.33E-07 8.33E-07
vg0709448532 sf0709447538 7 9448532 1.33E-06 1.33E-06
vg0521872068 sf0521809510 5 21872068 1.60E-06 1.60E-06
vg0404029438 sf0404025045 4 4029438 2.10E-06 2.10E-06
vg0421344668 sf0421172722 4 21344668 2.15E-06 2.15E-06
vg0623981969 sf0623980972 6 23981969 2.24E-06 2.24E-06
vg0515278523 sf0515221064 5 15278523 2.51E-06 2.51E-06
vg0715502728 sf0715501735 7 15502728 3.68E-06 3.68E-06
vg0817557507 sf0817554793 8 17557507 4.47E-06 4.47E-06