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 mr1085 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
vg0719135307 sf0719134314 7 19135307 7.80E-51 3.22E-23
vg0719303206 sf0719302213 7 19303206 8.00E-51 1.02E-27
vg0706906002 sf0706905007 7 6906002 2.78E-36 6.04E-06
vg0305007501 sf0305006503 3 5007501 5.22E-36 NA
vg0917918788 sf0917917787 9 17918788 2.07E-34 NA
vg0704136341 sf0704135342 7 4136341 3.27E-34 NA
vg0305247107 sf0305246107 3 5247107 2.88E-33 2.39E-07
vg0216222513 sf0216216643 2 16222513 6.00E-33 1.07E-06
vg0315157973 sf0315156620 3 15157973 1.62E-30 7.00E-07
vg0719091461 sf0719090468 7 19091461 NA 3.37E-20
vg0719413496 sf0719412503 7 19413496 NA 5.83E-19
vg0719071513 sf0719070520 7 19071513 NA 1.97E-15
vg0719208973 sf0719207980 7 19208973 NA 1.53E-13
vg0719345198 sf0719344205 7 19345198 NA 1.13E-11
vg0719041739 sf0719040746 7 19041739 NA 2.70E-11
vg0719466615 sf0719465622 7 19466615 NA 5.01E-10
vg0329561125 sf0329554165 3 29561125 NA 5.21E-10
vg1217507757 sf1217501712 12 17507757 NA 1.47E-08
vg0720529894 sf0720528901 7 20529894 NA 4.94E-08
vg0707699197 sf0707698202 7 7699197 NA 6.12E-08
vg0428494128 sf0428308982 4 28494128 NA 1.24E-07
vg0233012400 sf0233006531 2 33012400 NA 1.64E-07
vg0109818394 sf0109817370 1 9818394 NA 2.85E-07
vg1100676096 sf1100675099 11 676096 NA 4.20E-07
vg0719436399 sf0719435406 7 19436399 NA 4.86E-07
vg0800947956 sf0800946958 8 947956 NA 6.31E-07
vg1213935504 sf1213932842 12 13935504 NA 6.66E-07
vg0716738061 sf0716737068 7 16738061 NA 6.93E-07
vg0909775480 sf0909774479 9 9775480 NA 7.31E-07
vg0107188867 sf0107187867 1 7188867 NA 1.09E-06
vg0402499668 sf0402495269 4 2499668 NA 6.90E-06
vg0603483013 sf0603482014 6 3483013 NA 7.22E-06