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 mr1695 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
vg1115159539 sf1114695853 11 15159539 5.57E-09 3.08E-07
vg0828279465 sf0828276751 8 28279465 2.16E-08 7.84E-06
vg0604641320 sf0604640321 6 4641320 2.49E-08 NA
vg0315566044 sf0315564691 3 15566044 6.99E-08 NA
vg0906928402 sf0906927402 9 6928402 9.06E-08 NA
vg0503364634 sf0503364611 5 3364634 1.31E-07 2.36E-06
vg0308082029 sf0308080967 3 8082029 3.14E-07 3.23E-06
vg0114940313 sf0114939287 1 14940313 4.24E-07 4.16E-06
vg0107647091 sf0107646091 1 7647091 1.16E-06 7.55E-07
vg1125038483 sf1124572323 11 25038483 2.98E-06 3.40E-07
vg0904240223 sf0904239223 9 4240223 NA 1.65E-06