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 mr1669 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
vg0901536604 sf0901535604 9 1536604 6.87E-08 6.87E-08
vg0321576069 sf0321574579 3 21576069 1.15E-07 1.15E-07
vg0219780702 sf0219774834 2 19780702 6.28E-07 6.28E-07
vg0203433343 sf0203433341 2 3433343 8.12E-07 8.12E-07
vg0322174837 sf0322173344 3 22174837 8.71E-07 8.71E-07
vg0124114465 sf0124113421 1 24114465 1.08E-06 1.08E-06
vg0220941584 sf0220935716 2 20941584 1.16E-06 1.16E-06
vg0222337580 sf0222331711 2 22337580 2.59E-06 2.59E-06
vg0205924397 sf0205924397 2 5924397 2.68E-06 2.68E-06
vg0610852582 sf0610851583 6 10852582 2.81E-06 2.81E-06
vg0329703696 sf0329696736 3 29703696 3.22E-06 3.22E-06
vg0431677153 sf0431492046 4 31677153 4.02E-06 4.02E-06
vg0333120209 sf0333113079 3 33120209 4.03E-06 4.03E-06
vg0417258890 sf0417086931 4 17258890 4.41E-06 4.41E-06
vg1203245777 sf1203244780 12 3245777 4.54E-06 4.54E-06
vg0220287168 sf0220281300 2 20287168 4.87E-06 4.87E-06
vg0819431872 sf0819429159 8 19431872 4.89E-06 4.89E-06
vg0706176980 sf0706175981 7 6176980 4.90E-06 4.90E-06