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 mr1561 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
vg1121410783 sf1120944660 11 21410783 5.37E-09 3.19E-07
vg1121559924 sf1121093801 11 21559924 7.92E-09 2.42E-07
vg0901631141 sf0901630141 9 1631141 3.37E-08 7.90E-07
vg0112495464 sf0112494438 1 12495464 1.52E-07 4.82E-06
vg0425395594 sf0425210455 4 25395594 2.65E-06 NA
vg0220789608 sf0220783740 2 20789608 3.16E-06 NA