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 mr1741 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
vg0114081823 sf0114080797 1 14081823 1.82E-09 2.99E-07
vg0114116382 sf0114115356 1 14116382 6.11E-09 2.79E-07
vg1118314742 sf1117848600 11 18314742 1.22E-08 1.28E-06
vg1117584893 sf1117118750 11 17584893 2.48E-08 NA
vg1117481063 sf1117014918 11 17481063 2.61E-08 NA
vg0500645272 sf0500645272 5 645272 3.43E-08 NA
vg0622823121 sf0622822124 6 22823121 1.14E-07 1.71E-06
vg1109901210 sf1109895787 11 9901210 2.63E-07 8.30E-07
vg0502090757 sf0502090739 5 2090757 2.52E-06 NA
vg1208053849 sf1208051255 12 8053849 5.26E-06 3.71E-06