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 mr1744 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
vg0400897236 sf0400896236 4 897236 1.06E-08 1.06E-08
vg1226265159 sf1226231553 12 26265159 5.49E-08 5.49E-08
vg0224644316 sf0224638447 2 24644316 7.59E-07 7.59E-07
vg1014164008 sf1014092774 10 14164008 3.08E-06 3.08E-06
vg1123141598 sf1122675469 11 23141598 3.13E-06 3.13E-06
vg0515363032 sf0515305573 5 15363032 3.16E-06 3.16E-06
vg1101700310 sf1101699311 11 1700310 4.17E-06 4.17E-06
vg0328066679 sf0328059733 3 28066679 4.23E-06 4.23E-06
vg1017856575 sf1017785348 10 17856575 4.49E-06 4.49E-06