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 mr1800 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
vg0432450435 sf0432265327 4 32450435 1.14E-29 1.60E-18
vg0432523372 sf0432338264 4 32523372 1.87E-27 2.26E-20
vg1019052626 sf1018981183 10 19052626 1.12E-20 NA
vg0204534958 sf0204534955 2 4534958 2.02E-17 3.12E-06
vg0432624995 sf0432439885 4 32624995 5.38E-17 5.70E-11
vg0402172536 sf0402168131 4 2172536 3.17E-16 NA
vg0128333724 sf0128332680 1 28333724 4.01E-16 NA
vg1018578760 sf1018507317 10 18578760 7.01E-16 2.79E-06
vg0131779850 sf0131778806 1 31779850 2.51E-15 NA
vg1018526508 sf1018455065 10 18526508 3.56E-15 6.75E-07
vg0432600246 sf0432415137 4 32600246 NA 6.56E-15
vg0432588212 sf0432403103 4 32588212 NA 3.12E-11
vg0431489327 sf0431304225 4 31489327 NA 5.23E-08
vg0432418113 sf0432233004 4 32418113 NA 2.09E-06
vg1125669886 sf1125203725 11 25669886 NA 2.56E-06
vg0413417765 sf0413408479 4 13417765 NA 2.70E-06
vg0805048816 sf0805047819 8 5048816 NA 3.38E-06
vg0518984986 sf0518922470 5 18984986 NA 3.49E-06
vg0434511632 sf0434326525 4 34511632 NA 3.81E-06
vg0820890632 sf0820887919 8 20890632 NA 6.09E-06
vg0804860838 sf0804859841 8 4860838 NA 7.26E-06