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 mr1907 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
vg0524737028 sf0524674449 5 24737028 5.75E-59 2.48E-33
vg0524744488 sf0524681909 5 24744488 1.88E-34 8.34E-10
vg1100512559 sf1100511562 11 512559 1.75E-21 NA
vg0524329978 sf0524267397 5 24329978 1.43E-20 8.59E-07
vg1122446629 sf1121980500 11 22446629 1.64E-17 3.26E-07
vg1205231921 sf1205230907 12 5231921 3.20E-17 1.02E-09
vg1100325847 sf1100324849 11 325847 4.95E-16 8.55E-08
vg0600140599 sf0600139599 6 140599 8.89E-14 1.51E-06
vg1122459168 sf1121993039 11 22459168 1.56E-12 9.76E-09
vg0526374896 sf0526312259 5 26374896 NA 3.10E-07
vg0520840504 sf0520777945 5 20840504 NA 5.44E-07
vg1110164978 sf1110159555 11 10164978 NA 1.11E-06
vg0818051791 sf0818049078 8 18051791 NA 3.37E-06
vg1108799422 sf1108794032 11 8799422 NA 4.29E-06
vg1216081981 sf1216079277 12 16081981 NA 8.96E-06