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 mr1911 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
vg0222743526 sf0222737657 2 22743526 6.69E-34 4.21E-32
vg0222724011 sf0222718142 2 22724011 3.25E-33 2.10E-34
vg0222725003 sf0222719134 2 22725003 6.06E-30 7.67E-15
vg0906971590 sf0906970590 9 6971590 6.57E-25 NA
vg1005768684 sf1005785222 10 5768684 2.38E-23 NA
vg0526059096 sf0525996516 5 26059096 2.49E-23 NA
vg0222681985 sf0222676116 2 22681985 NA 4.26E-11
vg0224552398 sf0224546529 2 24552398 NA 8.22E-10
vg0224832469 sf0224826600 2 24832469 NA 4.15E-07
vg0222672641 sf0222666772 2 22672641 NA 5.29E-07
vg0223663745 sf0223657876 2 23663745 NA 6.53E-07
vg0222634177 sf0222628308 2 22634177 NA 1.12E-06
vg0223747954 sf0223742085 2 23747954 NA 1.23E-06
vg0224233133 sf0224227264 2 24233133 NA 2.59E-06
vg0218580570 sf0218574701 2 18580570 NA 3.29E-06
vg0222735022 sf0222729153 2 22735022 NA 3.47E-06
vg0222629829 sf0222623960 2 22629829 NA 4.23E-06
vg0302217186 sf0302216182 3 2217186 NA 4.59E-06