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 mr1110 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
vg0610559165 sf0610558166 6 10559165 7.89E-35 3.82E-16
vg0610459123 sf0610458124 6 10459123 2.31E-31 1.05E-16
vg0610360715 sf0610359716 6 10360715 2.61E-18 1.71E-10
vg0610412049 sf0610411050 6 10412049 3.74E-16 9.56E-09
vg0609930953 sf0609929954 6 9930953 5.71E-15 2.75E-07
vg0617359224 sf0617358227 6 17359224 2.27E-14 NA
vg0610683007 sf0610682008 6 10683007 3.60E-14 1.94E-09
vg0820386017 sf0820383304 8 20386017 1.48E-13 NA
vg0610683043 sf0610682044 6 10683043 2.03E-13 2.19E-08
vg0611946117 sf0611945118 6 11946117 1.41E-12 7.16E-07
vg0610393322 sf0610392323 6 10393322 1.72E-08 4.76E-06
vg0610642043 sf0610641044 6 10642043 1.09E-07 1.72E-07
vg1007787923 sf1007803533 10 7787923 NA 4.34E-08
vg1009114642 sf1009043503 10 9114642 NA 1.40E-07
vg1002973972 sf1002972949 10 2973972 NA 9.56E-07
vg1008033341 sf1008010896 10 8033341 NA 9.83E-07
vg0528706863 sf0528644218 5 28706863 NA 3.08E-06
vg0825168532 sf0825165818 8 25168532 NA 4.43E-06
vg0520363169 sf0520300642 5 20363169 NA 7.49E-06
vg1007752268 sf1007767877 10 7752268 NA 8.75E-06