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 mr1234 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
vg0610566084 sf0610565085 6 10566084 4.95E-125 1.77E-44
vg0610566343 sf0610565344 6 10566343 5.99E-125 6.34E-45
vg0610481003 sf0610480004 6 10481003 2.72E-113 7.06E-34
vg0616950705 sf0616949708 6 16950705 7.91E-76 NA
vg0719259692 sf0719258699 7 19259692 5.82E-71 NA
vg0304920678 sf0304919680 3 4920678 1.22E-69 NA
vg0627242607 sf0627241610 6 27242607 6.88E-68 NA
vg0617319066 sf0617318069 6 17319066 1.01E-62 5.68E-08
vg0610028912 sf0610027913 6 10028912 NA 7.15E-18
vg0610444069 sf0610443070 6 10444069 NA 5.08E-15
vg0610778299 sf0610777300 6 10778299 NA 1.09E-13
vg0611682950 sf0611681951 6 11682950 NA 3.90E-12
vg0610107722 sf0610106723 6 10107722 NA 6.00E-11
vg0610585154 sf0610584155 6 10585154 NA 1.21E-10
vg0610069455 sf0610068456 6 10069455 NA 1.44E-09
vg0609889743 sf0609888744 6 9889743 NA 1.37E-08
vg0611127784 sf0611126785 6 11127784 NA 1.78E-08
vg0610021530 sf0610020531 6 10021530 NA 2.55E-08
vg0613057898 sf0613056899 6 13057898 NA 2.89E-08
vg0614543893 sf0614542894 6 14543893 NA 3.77E-08
vg0610924794 sf0610923795 6 10924794 NA 5.03E-08
vg0611912637 sf0611911638 6 11912637 NA 1.60E-07
vg0610393322 sf0610392323 6 10393322 NA 1.64E-07
vg0609207468 sf0609206469 6 9207468 NA 4.03E-07
vg0920307704 sf0920307223 9 20307704 NA 5.69E-07
vg0619171840 sf0619170843 6 19171840 NA 7.56E-07
vg0613124492 sf0613123493 6 13124492 NA 8.62E-07