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 mr1932 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
vg0307466215 sf0307465153 3 7466215 1.34E-40 1.90E-06
vg0504766113 sf0504766090 5 4766113 2.59E-39 3.21E-06
vg0322554729 sf0322553218 3 22554729 2.06E-38 NA
vg0620907082 sf0620906085 6 20907082 2.53E-38 NA
vg0412929168 sf0412919878 4 12929168 3.24E-38 NA
vg0724691849 sf0724690855 7 24691849 NA 1.68E-09
vg1001190961 sf1001189938 10 1190961 NA 1.12E-07
vg0504773265 sf0504773242 5 4773265 NA 1.27E-07
vg0124405341 sf0124404297 1 24405341 NA 2.62E-07
vg1001167572 sf1001166548 10 1167572 NA 4.43E-07
vg0724771428 sf0724770434 7 24771428 NA 1.23E-06
vg0724482522 sf0724481528 7 24482522 NA 1.83E-06
vg1213714850 sf1213712188 12 13714850 NA 2.26E-06
vg0124403552 sf0124402508 1 24403552 NA 2.70E-06
vg1011645008 sf1011573823 10 11645008 NA 3.21E-06