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 mr1150 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
vg0222746050 sf0222740181 2 22746050 8.65E-101 1.46E-41
vg0222723992 sf0222718123 2 22723992 2.19E-98 1.04E-41
vg1223579855 sf1223546315 12 23579855 1.28E-39 NA
vg0917469028 sf0917468027 9 17469028 3.63E-37 NA
vg0722942800 sf0722941807 7 22942800 1.39E-35 NA
vg0602733915 sf0602732916 6 2733915 2.06E-35 NA
vg0222725003 sf0222719134 2 22725003 NA 7.24E-16
vg0222648545 sf0222642676 2 22648545 NA 6.94E-13
vg0222653409 sf0222647540 2 22653409 NA 9.74E-12
vg0224552398 sf0224546529 2 24552398 NA 1.32E-10
vg0223663745 sf0223657876 2 23663745 NA 1.59E-08
vg0222271516 sf0222265647 2 22271516 NA 2.91E-08
vg0712392714 sf0712391721 7 12392714 NA 5.05E-08
vg0907026290 sf0907025290 9 7026290 NA 5.49E-08
vg0223736835 sf0223730966 2 23736835 NA 8.52E-08
vg0224878279 sf0224872410 2 24878279 NA 1.12E-07
vg0223883799 sf0223877930 2 23883799 NA 1.41E-07
vg0224246969 sf0224241100 2 24246969 NA 1.53E-07
vg0222681985 sf0222676116 2 22681985 NA 2.38E-07
vg0222729132 sf0222723263 2 22729132 NA 2.50E-07
vg0222041029 sf0222035160 2 22041029 NA 2.81E-07
vg0224832469 sf0224826600 2 24832469 NA 4.45E-07
vg0214216570 sf0214210700 2 14216570 NA 1.12E-06
vg0218580570 sf0218574701 2 18580570 NA 1.32E-06
vg0224788519 sf0224782650 2 24788519 NA 1.39E-06
vg0204905017 sf0204905014 2 4905017 NA 1.78E-06
vg0827202728 sf0827200014 8 27202728 NA 2.08E-06
vg0222558409 sf0222552540 2 22558409 NA 2.38E-06
vg0512250003 sf0512249933 5 12250003 NA 3.57E-06