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 mr1861 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
vg0222727819 sf0222721950 2 22727819 1.23E-87 9.70E-31
vg0222718166 sf0222712297 2 22718166 4.65E-87 1.11E-31
vg0705306490 sf0705305491 7 5306490 2.58E-63 NA
vg0626745994 sf0626744997 6 26745994 3.47E-62 NA
vg0304830712 sf0304829714 3 4830712 1.15E-60 NA
vg0917464010 sf0917463009 9 17464010 3.84E-59 NA
vg0522357374 sf0522294815 5 22357374 4.38E-54 3.24E-07
vg0222725003 sf0222719134 2 22725003 NA 7.09E-12
vg0223721789 sf0223715920 2 23721789 NA 1.58E-10
vg0224294117 sf0224288248 2 24294117 NA 1.10E-07
vg0223720170 sf0223714301 2 23720170 NA 1.50E-07
vg0207693964 sf0220933879 2 7693964 NA 4.49E-07
vg0311437556 sf0311436274 3 11437556 NA 4.75E-07
vg0209234214 sf0209234212 2 9234214 NA 1.71E-06
vg0121061296 sf0121060251 1 21061296 NA 2.02E-06
vg0223663745 sf0223657876 2 23663745 NA 2.04E-06
vg0224293556 sf0224287687 2 24293556 NA 2.29E-06
vg0222716080 sf0222710211 2 22716080 NA 2.51E-06
vg0223211906 sf0223206037 2 23211906 NA 3.14E-06
vg0224242820 sf0224236951 2 24242820 NA 3.46E-06
vg0402151540 sf0402147135 4 2151540 NA 7.41E-06