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 mr1373 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
vg0805005643 sf0805004646 8 5005643 2.56E-09 2.56E-09
vg0329703696 sf0329696736 3 29703696 4.91E-08 4.91E-08
vg0321576069 sf0321574579 3 21576069 1.15E-07 1.15E-07
vg0107079035 sf0107078035 1 7079035 2.26E-07 2.26E-07
vg0500776377 sf0500776359 5 776377 3.98E-07 3.98E-07
vg0124420479 sf0124419435 1 24420479 4.72E-07 4.72E-07
vg0206578247 sf0206578247 2 6578247 5.29E-07 5.29E-07
vg0219780702 sf0219774834 2 19780702 8.09E-07 8.09E-07
vg0222337580 sf0222331711 2 22337580 1.07E-06 1.07E-06
vg0808428148 sf0808427152 8 8428148 1.41E-06 1.41E-06
vg0140888404 sf0140887361 1 40888404 2.48E-06 2.48E-06
vg0706732811 sf0706731816 7 6732811 2.51E-06 2.51E-06
vg0826077942 sf0826075228 8 26077942 2.74E-06 2.74E-06
vg0714140419 sf0714139426 7 14140419 3.80E-06 3.80E-06
vg0205924397 sf0205924397 2 5924397 3.99E-06 3.99E-06
vg1020531763 sf1020460242 10 20531763 4.06E-06 4.07E-06
vg0701495062 sf0701494062 7 1495062 4.29E-06 4.29E-06