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 mr1688 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
vg0321576069 sf0321574579 3 21576069 1.89E-08 1.89E-08
vg0805946030 sf0805945033 8 5946030 4.85E-08 4.85E-08
vg0804905723 sf0804904726 8 4905723 1.88E-07 1.88E-07
vg0107079035 sf0107078035 1 7079035 1.94E-07 1.94E-07
vg0222337580 sf0222331711 2 22337580 2.66E-07 2.67E-07
vg0901536604 sf0901535604 9 1536604 4.52E-07 4.52E-07
vg0610852582 sf0610851583 6 10852582 5.14E-07 5.14E-07
vg0124420479 sf0124419435 1 24420479 5.90E-07 5.91E-07
vg0329703696 sf0329696736 3 29703696 6.19E-07 6.19E-07
vg0206578247 sf0206578247 2 6578247 9.64E-07 9.65E-07
vg1127480350 sf1127008737 11 27480350 1.17E-06 1.17E-06
vg0219780702 sf0219774834 2 19780702 1.25E-06 1.25E-06
vg0826077942 sf0826075228 8 26077942 1.46E-06 1.46E-06
vg1020531779 sf1020460258 10 20531779 2.51E-06 2.51E-06
vg0333120209 sf0333113079 3 33120209 3.49E-06 3.49E-06
vg0900843348 sf0900842348 9 843348 3.79E-06 3.79E-06
vg0501764750 sf0501764733 5 1764750 4.01E-06 4.01E-06
vg0113510414 sf0113509388 1 13510414 4.16E-06 4.16E-06