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 mr1843 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 3.76E-09 3.76E-09
vg0805946030 sf0805945033 8 5946030 3.58E-08 3.58E-08
vg0124420479 sf0124419435 1 24420479 7.14E-08 7.15E-08
vg1020531779 sf1020460258 10 20531779 8.49E-08 8.49E-08
vg0826077942 sf0826075228 8 26077942 2.51E-07 2.51E-07
vg0610852582 sf0610851583 6 10852582 2.82E-07 2.82E-07
vg0329703696 sf0329696736 3 29703696 2.96E-07 2.96E-07
vg1013161872 sf1013090643 10 13161872 7.61E-07 7.61E-07
vg0804905723 sf0804904726 8 4905723 8.42E-07 8.42E-07
vg1116613245 sf1116148123 11 16613245 9.38E-07 9.38E-07
vg0206578247 sf0206578247 2 6578247 9.97E-07 9.97E-07
vg0220358695 sf0220352827 2 20358695 1.22E-06 1.22E-06
vg0113510414 sf0113509388 1 13510414 1.30E-06 1.30E-06
vg0629600574 sf0629599576 6 29600574 1.55E-06 1.55E-06
vg0900843849 sf0900842849 9 843849 1.61E-06 1.61E-06
vg0222337580 sf0222331711 2 22337580 1.62E-06 1.62E-06
vg0724377253 sf0724376259 7 24377253 2.39E-06 2.39E-06
vg1001247868 sf1001246845 10 1247868 2.81E-06 2.81E-06
vg0218569230 sf0218563361 2 18569230 2.92E-06 2.92E-06
vg0107079035 sf0107078035 1 7079035 3.26E-06 3.26E-06