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 mr1124 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
vg0222725905 sf0222720036 2 22725905 7.17E-77 1.64E-53
vg0222700046 sf0222694177 2 22700046 3.85E-18 3.40E-15
vg0222661859 sf0222655990 2 22661859 1.75E-17 1.33E-16
vg0223825635 sf0223819766 2 23825635 5.42E-17 2.35E-08
vg0224679366 sf0224673497 2 24679366 8.94E-17 1.02E-09
vg0122532559 sf0122531514 1 22532559 3.74E-16 NA
vg0224678754 sf0224672885 2 24678754 1.28E-15 4.84E-10
vg0224832365 sf0224826496 2 24832365 3.06E-15 5.73E-09
vg0610592581 sf0610591582 6 10592581 5.56E-15 5.16E-10
vg0223663746 sf0223657877 2 23663746 8.73E-15 4.54E-11
vg0610597911 sf0610596912 6 10597911 3.28E-14 3.21E-10
vg0223947818 sf0223941949 2 23947818 1.22E-13 1.71E-06
vg1112606104 sf1112142307 11 12606104 1.93E-12 3.67E-07
vg0224382271 sf0224376402 2 24382271 1.30E-10 6.89E-08
vg0222857256 sf0222851387 2 22857256 1.63E-10 1.30E-09
vg0223166690 sf0223160821 2 23166690 1.68E-09 1.25E-06
vg0224110296 sf0224104427 2 24110296 4.54E-08 3.43E-07
vg0610641076 sf0610640077 6 10641076 NA 1.53E-07
vg0223526274 sf0223520405 2 23526274 NA 3.38E-07
vg0223013382 sf0223007513 2 23013382 NA 4.05E-07
vg0224832469 sf0224826600 2 24832469 NA 7.22E-07
vg0222390817 sf0222384948 2 22390817 NA 8.74E-07
vg0922295660 sf0922295179 9 22295660 NA 1.39E-06
vg0223926024 sf0223920155 2 23926024 NA 1.52E-06
vg0142773064 sf0142772020 1 42773064 NA 1.81E-06