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 mr1626 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
vg0405535697 sf0405531138 4 5535697 6.72E-32 2.97E-18
vg0405589223 sf0405584664 4 5589223 1.95E-31 3.05E-19
vg0405465111 sf0405460552 4 5465111 2.68E-17 4.71E-09
vg0410985561 sf0410976262 4 10985561 1.11E-16 5.05E-10
vg0710469439 sf0710468445 7 10469439 2.43E-15 NA
vg0807415288 sf0807414293 8 7415288 2.90E-15 NA
vg0405682716 sf0405678155 4 5682716 5.70E-15 4.47E-13
vg0706194043 sf0706193044 7 6194043 6.59E-14 3.44E-06
vg0423550995 sf0423365852 4 23550995 7.26E-14 NA
vg0405309804 sf0405305245 4 5309804 8.23E-13 1.14E-07
vg0406028647 sf0406024086 4 6028647 1.04E-12 3.03E-07
vg0604119299 sf0604118300 6 4119299 2.27E-12 3.92E-06
vg0412751761 sf0412742471 4 12751761 6.46E-12 1.55E-06
vg0405559687 sf0405555128 4 5559687 NA 1.95E-12
vg0405440340 sf0405435781 4 5440340 NA 1.91E-08
vg0405244442 sf0405239883 4 5244442 NA 1.00E-06
vg0409017235 sf0409012510 4 9017235 NA 1.61E-06
vg0407116784 sf0407112054 4 7116784 NA 1.74E-06
vg0702672533 sf0702671534 7 2672533 NA 2.38E-06
vg0804004654 sf0804003657 8 4004654 NA 2.43E-06
vg0405785336 sf0405780775 4 5785336 NA 2.65E-06
vg0626718957 sf0626717960 6 26718957 NA 3.08E-06