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 mr1088 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
vg0719011406 sf0719010413 7 19011406 2.57E-106 3.56E-21
vg0704138796 sf0704137797 7 4138796 2.91E-88 NA
vg1201930768 sf1201929766 12 1930768 3.68E-85 7.93E-06
vg0706871631 sf0706870636 7 6871631 1.84E-84 NA
vg0917918788 sf0917917787 9 17918788 3.81E-84 NA
vg0719199004 sf0719198011 7 19199004 2.36E-81 7.57E-30
vg0706507299 sf0706506304 7 6507299 7.86E-78 2.39E-06
vg1202102394 sf1202101392 12 2102394 1.22E-77 3.17E-06
vg0612891258 sf0612890259 6 12891258 1.27E-76 NA
vg0802300931 sf0802299934 8 2300931 2.08E-75 NA
vg0719091461 sf0719090468 7 19091461 NA 1.08E-21
vg0719141196 sf0719140203 7 19141196 NA 9.87E-17
vg0718955684 sf0718954691 7 18955684 NA 5.35E-12
vg0719071513 sf0719070520 7 19071513 NA 2.17E-11
vg0719087589 sf0719086596 7 19087589 NA 1.37E-10
vg0719618102 sf0719617109 7 19618102 NA 3.08E-09
vg0719466615 sf0719465622 7 19466615 NA 1.43E-08
vg0719417123 sf0719416130 7 19417123 NA 4.02E-08
vg0305031973 sf0305030975 3 5031973 NA 3.21E-07
vg0718911344 sf0718910351 7 18911344 NA 6.79E-07
vg0315177161 sf0315175808 3 15177161 NA 8.42E-07
vg0719345198 sf0719344205 7 19345198 NA 1.03E-06
vg0718983313 sf0718982320 7 18983313 NA 1.10E-06
vg0718961954 sf0718960961 7 18961954 NA 1.26E-06
vg0705591916 sf0705590917 7 5591916 NA 1.36E-06
vg0828393303 sf0828390589 8 28393303 NA 1.37E-06
vg0719527870 sf0719526877 7 19527870 NA 1.39E-06
vg0315228337 sf0315226984 3 15228337 NA 2.38E-06
vg0719601158 sf0719600165 7 19601158 NA 3.02E-06
vg0719016083 sf0719015090 7 19016083 NA 3.57E-06
vg0722032999 sf0722032006 7 22032999 NA 3.60E-06
vg0813135425 sf0813132985 8 13135425 NA 3.74E-06