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 mr1793 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
vg0919909956 sf0919909475 9 19909956 2.59E-61 1.37E-12
vg0720543817 sf0720542824 7 20543817 1.31E-55 NA
vg0607237460 sf0607236461 6 7237460 1.59E-55 NA
vg0704344209 sf0704343210 7 4344209 4.26E-55 NA
vg0327119904 sf0327112957 3 27119904 1.30E-53 NA
vg0919970662 sf0919970181 9 19970662 NA 7.07E-12
vg0202698817 sf0202698815 2 2698817 NA 1.02E-08
vg0202719439 sf0202719437 2 2719439 NA 1.16E-07
vg0317038125 sf0317036999 3 17038125 NA 2.24E-07
vg0820479181 sf0820476468 8 20479181 NA 3.81E-07
vg0400357479 sf0400356479 4 357479 NA 7.90E-07
vg0207710652 sf0207710651 2 7710652 NA 1.75E-06
vg0132167342 sf0132166298 1 32167342 NA 1.88E-06
vg0430616892 sf0430431767 4 30616892 NA 1.89E-06
vg0625461059 sf0625460062 6 25461059 NA 2.31E-06
vg1220938287 sf1220904836 12 20938287 NA 3.10E-06
vg0203405727 sf0203405725 2 3405727 NA 3.63E-06
vg0400002670 sf0400001670 4 2670 NA 3.76E-06
vg1022548815 sf1022477289 10 22548815 NA 4.33E-06
vg1017856339 sf1017785112 10 17856339 NA 4.62E-06