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 mr1682 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
vg0917565197 sf0917564196 9 17565197 6.83E-42 NA
vg0914739778 sf0914738777 9 14739778 1.90E-40 NA
vg0922500124 sf0922499643 9 22500124 3.27E-40 NA
vg0626081466 sf0626080469 6 26081466 4.63E-40 NA
vg1014200487 sf1014129253 10 14200487 1.00E-39 NA
vg1115099731 sf1114636045 11 15099731 1.36E-35 NA
vg0705702782 sf0705701783 7 5702782 NA 2.29E-09
vg1208638516 sf1208635923 12 8638516 NA 2.12E-07
vg0922324460 sf0922323979 9 22324460 NA 2.80E-07
vg1113156611 sf1112692932 11 13156611 NA 3.72E-07
vg1218022439 sf1217993875 12 18022439 NA 5.77E-07
vg0335630368 sf0335623237 3 35630368 NA 7.53E-07
vg1021514492 sf1021442969 10 21514492 NA 1.07E-06
vg0613699047 sf0613698048 6 13699047 NA 1.12E-06
vg0410038851 sf0410029548 4 10038851 NA 1.25E-06
vg0220953380 sf0220947512 2 20953380 NA 1.43E-06
vg0904461223 sf0904460223 9 4461223 NA 1.49E-06
vg0601213669 sf0601212670 6 1213669 NA 1.99E-06
vg0317255027 sf0317253837 3 17255027 NA 2.42E-06
vg0905240849 sf0905239849 9 5240849 NA 3.22E-06
vg0716748284 sf0716747291 7 16748284 NA 3.41E-06
vg0523768940 sf0523706361 5 23768940 NA 3.48E-06
vg0327530071 sf0327523124 3 27530071 NA 3.78E-06
vg0101342775 sf0101341775 1 1342775 NA 3.98E-06
vg1209066521 sf1209063930 12 9066521 NA 4.22E-06
vg0226125510 sf0226119641 2 26125510 NA 4.39E-06
vg1021514488 sf1021442965 10 21514488 NA 5.63E-06