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 mr1067 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
vg0610673914 sf0610672915 6 10673914 4.07E-79 5.21E-19
vg0610680325 sf0610679326 6 10680325 1.93E-78 3.76E-19
vg0610459123 sf0610458124 6 10459123 1.52E-71 5.00E-22
vg0222746228 sf0222740359 2 22746228 6.22E-59 3.63E-13
vg0616950705 sf0616949708 6 16950705 1.11E-56 NA
vg0122580922 sf0122579877 1 22580922 2.77E-54 NA
vg0719132379 sf0719131386 7 19132379 1.52E-52 NA
vg0617810167 sf0617809170 6 17810167 1.02E-49 2.29E-08
vg0222727819 sf0222721950 2 22727819 6.65E-48 4.00E-16
vg0222729090 sf0222723221 2 22729090 1.62E-45 7.35E-17
vg0223051176 sf0223045307 2 23051176 6.26E-45 4.43E-07
vg0609919357 sf0609918358 6 9919357 NA 1.41E-09
vg0223692838 sf0223686969 2 23692838 NA 1.82E-09
vg0610028912 sf0610027913 6 10028912 NA 2.12E-09
vg0225615391 sf0225609522 2 25615391 NA 6.57E-08
vg0614107939 sf0614106940 6 14107939 NA 8.46E-08
vg0611999588 sf0611998589 6 11999588 NA 1.64E-07
vg0610553003 sf0610552004 6 10553003 NA 2.14E-07
vg1112908978 sf1112445299 11 12908978 NA 2.47E-07
vg0222729853 sf0222723984 2 22729853 NA 3.21E-07
vg0713349047 sf0713348054 7 13349047 NA 9.03E-07
vg0610278393 sf0610277394 6 10278393 NA 1.17E-06
vg0222751236 sf0222745367 2 22751236 NA 1.30E-06
vg0211839911 sf0211839907 2 11839911 NA 1.56E-06
vg0224274396 sf0224268527 2 24274396 NA 1.91E-06
vg0610880175 sf0610879176 6 10880175 NA 2.65E-06
vg0222725003 sf0222719134 2 22725003 NA 2.69E-06
vg0105393860 sf0105392860 1 5393860 NA 2.70E-06
vg0610676484 sf0610675485 6 10676484 NA 3.72E-06
vg0120461276 sf0120460231 1 20461276 NA 3.73E-06
vg0610674740 sf0610673741 6 10674740 NA 3.96E-06
vg0630859532 sf0630858534 6 30859532 NA 5.63E-06