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 mr1616 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
vg0232486002 sf0232480133 2 32486002 2.43E-07 2.43E-07
vg0500807732 sf0500807714 5 807732 6.82E-07 6.82E-07
vg1102888595 sf1102884499 11 2888595 8.13E-07 8.13E-07
vg0726946590 sf0726945596 7 26946590 2.20E-06 2.20E-06
vg0329307188 sf0329300228 3 29307188 3.21E-06 3.21E-06
vg0334733257 sf0334726127 3 34733257 3.30E-06 3.30E-06
vg0222337580 sf0222331711 2 22337580 4.21E-06 4.21E-06
vg0309400270 sf0309399206 3 9400270 4.29E-06 4.30E-06
vg1126982731 sf1126511118 11 26982731 4.58E-06 4.58E-06