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 mr1585 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
vg0217108340 sf0217102470 2 17108340 4.68E-13 3.96E-08
vg0216650911 sf0216645041 2 16650911 6.23E-13 1.81E-09
vg0421453331 sf0421281382 4 21453331 2.46E-10 4.87E-06
vg0729047751 sf0729046759 7 29047751 4.34E-09 NA
vg0218261094 sf0218255225 2 18261094 8.74E-09 8.30E-09
vg1206971120 sf1206970010 12 6971120 1.66E-08 NA
vg0218680006 sf0218674137 2 18680006 1.96E-08 9.15E-08
vg0911050033 sf0911049032 9 11050033 5.35E-08 9.80E-07
vg0216873517 sf0216867647 2 16873517 1.44E-07 2.52E-09
vg1222089377 sf1222055924 12 22089377 5.27E-07 8.12E-07
vg0911061673 sf0911060672 9 11061673 2.07E-06 NA
vg0421084486 sf0420912539 4 21084486 5.45E-06 NA
vg0202282068 sf0202282066 2 2282068 7.66E-06 4.19E-06