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 mr1658 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
vg0803654150 sf0803653153 8 3654150 4.93E-15 2.90E-09
vg0401895360 sf0401890956 4 1895360 2.29E-13 1.17E-06
vg0724248089 sf0724247095 7 24248089 5.50E-13 NA
vg0134272325 sf0134271282 1 34272325 8.65E-13 3.86E-08
vg0917104880 sf0917103879 9 17104880 1.00E-12 NA
vg0137195833 sf0137194790 1 37195833 2.60E-12 8.80E-07
vg0618798718 sf0618797721 6 18798718 4.00E-12 1.29E-06
vg0618516900 sf0618515903 6 18516900 4.68E-11 8.11E-07
vg1105347465 sf1105343216 11 5347465 4.31E-10 4.73E-07
vg0803657241 sf0803656244 8 3657241 NA 7.32E-09
vg0713895071 sf0713894078 7 13895071 NA 1.02E-06
vg0709781857 sf0709780863 7 9781857 NA 2.60E-06
vg1104443245 sf1104439147 11 4443245 NA 2.92E-06
vg0219081199 sf0219075331 2 19081199 NA 3.47E-06
vg0218989953 sf0218984084 2 18989953 NA 3.88E-06
vg1004348990 sf1004365528 10 4348990 NA 4.00E-06
vg0917466490 sf0917465489 9 17466490 NA 4.68E-06