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 mr1674 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
vg0142427760 sf0142426716 1 42427760 8.99E-08 8.99E-08
vg1020531763 sf1020460242 10 20531763 1.28E-07 1.28E-07
vg0808428148 sf0808427152 8 8428148 1.54E-07 1.54E-07
vg0420718113 sf0420546156 4 20718113 2.00E-07 1.99E-07
vg0500918476 sf0500918459 5 918476 2.51E-07 2.52E-07
vg0220342715 sf0220336847 2 20342715 3.49E-07 3.50E-07
vg1020529341 sf1020457820 10 20529341 4.32E-07 4.32E-07
vg0630366621 sf0630365623 6 30366621 5.04E-07 5.05E-07
vg0801629021 sf0801628023 8 1629021 2.05E-06 2.05E-06
vg0217104494 sf0217098624 2 17104494 2.17E-06 2.17E-06
vg0221838070 sf0221832201 2 21838070 2.30E-06 2.29E-06
vg1213065934 sf1213063273 12 13065934 3.87E-06 3.87E-06
vg0404029438 sf0404025045 4 4029438 4.26E-06 4.25E-06
vg0606329912 sf0606328913 6 6329912 4.52E-06 4.52E-06
vg0516381476 sf0516323958 5 16381476 4.88E-06 4.87E-06