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 mr1608 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
vg0101139584 sf0101138584 1 1139584 1.24E-14 NA
vg0217269742 sf0217263872 2 17269742 2.49E-14 3.85E-06
vg0217852863 sf0217846994 2 17852863 4.12E-13 8.96E-08
vg0206827776 sf0206827776 2 6827776 4.23E-13 NA
vg0138561974 sf0138560931 1 38561974 6.34E-13 NA
vg0424091351 sf0423906212 4 24091351 6.64E-13 NA
vg0217864141 sf0217858272 2 17864141 6.66E-11 3.86E-06
vg1110542233 sf1110536778 11 10542233 1.80E-09 NA
vg1019408343 sf1019336898 10 19408343 NA 1.37E-07
vg0605857548 sf0605856549 6 5857548 NA 1.19E-06
vg0704019475 sf0704018476 7 4019475 NA 4.59E-06
vg1103239153 sf1103235056 11 3239153 NA 4.68E-06