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 mr1242 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
vg0610674764 sf0610673765 6 10674764 1.08E-15 4.09E-06
vg0610429989 sf0610428990 6 10429989 2.12E-15 7.31E-07
vg0621076898 sf0621075901 6 21076898 2.68E-11 NA
vg0230005440 sf0229999571 2 30005440 1.31E-10 NA
vg0616930719 sf0616929722 6 16930719 5.92E-10 NA
vg0629496844 sf0629495846 6 29496844 1.39E-09 NA
vg0229918162 sf0229912293 2 29918162 1.26E-07 NA
vg0225037452 sf0225031583 2 25037452 1.26E-06 3.05E-06
vg1124985840 sf1124519680 11 24985840 1.30E-06 NA
vg0408965989 sf0408961265 4 8965989 1.33E-06 3.57E-06
vg1002434615 sf1002433592 10 2434615 1.97E-06 2.23E-06
vg0920451675 sf0920451194 9 20451675 NA 4.89E-09
vg0139807295 sf0139806252 1 39807295 NA 1.17E-07
vg0526662708 sf0526600066 5 26662708 NA 2.67E-07
vg0315572376 sf0315571023 3 15572376 NA 4.62E-07
vg0220169570 sf0220163702 2 20169570 NA 6.10E-07
vg1208788061 sf1208785468 12 8788061 NA 8.57E-07
vg0220941661 sf0220935793 2 20941661 NA 1.57E-06
vg0223876122 sf0223870253 2 23876122 NA 1.89E-06
vg0326244581 sf0326242600 3 26244581 NA 2.45E-06
vg1125768577 sf1125302416 11 25768577 NA 2.81E-06
vg1127281051 sf1126809438 11 27281051 NA 4.03E-06
vg0427823476 sf0427638336 4 27823476 NA 5.69E-06