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 mr1630 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
vg0318856031 sf0318854791 3 18856031 6.29E-08 6.29E-08
vg0626920669 sf0626919672 6 26920669 8.14E-08 8.14E-08
vg0415473298 sf0415463981 4 15473298 2.99E-07 2.99E-07
vg0714475265 sf0714474272 7 14475265 3.06E-07 3.06E-07
vg0921954182 sf0921953701 9 21954182 5.53E-07 5.53E-07
vg0228241702 sf0228235833 2 28241702 7.20E-07 7.20E-07
vg1001912776 sf1001911753 10 1912776 7.59E-07 7.59E-07
vg1215339513 sf1215336811 12 15339513 8.17E-07 8.17E-07
vg1019533706 sf1019462230 10 19533706 1.06E-06 1.06E-06
vg0230805438 sf0230799569 2 30805438 2.20E-06 2.20E-06
vg1213425621 sf1213422959 12 13425621 3.19E-06 3.19E-06