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 mr1546 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
vg1215854982 sf1215852278 12 15854982 3.07E-31 3.08E-15
vg1210300519 sf1210297932 12 10300519 3.80E-31 1.75E-13
vg1209294462 sf1209291871 12 9294462 9.59E-30 1.68E-14
vg1223872832 sf1223839285 12 23872832 2.02E-22 1.49E-07
vg1212726422 sf1212723761 12 12726422 5.21E-18 1.28E-06
vg1207616892 sf1207614298 12 7616892 3.24E-17 3.67E-06
vg1017701671 sf1017630444 10 17701671 1.06E-16 NA
vg1217600161 sf1217594116 12 17600161 2.63E-15 5.92E-07
vg0217670144 sf0217664274 2 17670144 8.89E-14 2.23E-06