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 mr1871 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
vg0221812870 sf0221807001 2 21812870 5.28E-35 1.30E-22
vg1119397311 sf1118930999 11 19397311 4.57E-24 5.62E-13
vg0310049531 sf0310048467 3 10049531 1.02E-21 3.93E-11
vg0629150340 sf0629149342 6 29150340 1.86E-21 1.26E-11
vg0309968802 sf0309967738 3 9968802 5.51E-21 1.76E-11
vg1107886187 sf1107881932 11 7886187 1.87E-20 3.88E-10
vg0400577517 sf0400576517 4 577517 3.40E-20 3.94E-08
vg0131776643 sf0131775599 1 31776643 1.21E-19 5.43E-10
vg0129396983 sf0129395938 1 29396983 3.02E-19 4.31E-10
vg0302037650 sf0302036646 3 2037650 3.14E-19 1.64E-07
vg1016920322 sf1016849094 10 16920322 3.15E-19 8.56E-08
vg0919091003 sf0919090592 9 19091003 5.32E-19 1.81E-07
vg0335650235 sf0335643104 3 35650235 7.05E-19 4.59E-09
vg0210298226 sf0210298224 2 10298226 2.22E-18 4.13E-08
vg0126344348 sf0126343304 1 26344348 4.00E-18 6.29E-09
vg0825703185 sf0825700471 8 25703185 3.05E-17 2.66E-07
vg1118303285 sf1117837144 11 18303285 3.06E-17 2.74E-07
vg0906782983 sf0906781983 9 6782983 2.09E-16 9.49E-08
vg0322395432 sf0322393921 3 22395432 1.73E-15 2.23E-07
vg0113340332 sf0113339306 1 13340332 1.32E-14 5.94E-08
vg0630043980 sf0630042982 6 30043980 NA 2.76E-08
vg0128084573 sf0128083529 1 28084573 NA 7.49E-08
vg1203501263 sf1203500264 12 3501263 NA 1.75E-07
vg1016576326 sf1016505099 10 16576326 NA 1.98E-07