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 mr1974 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
vg0142695483 sf0142694439 1 42695483 9.49E-20 2.31E-12
vg0141599281 sf0141598238 1 41599281 6.24E-11 4.61E-06
vg0104472484 sf0104471484 1 4472484 9.66E-11 NA
vg0142144554 sf0142143511 1 42144554 2.32E-10 4.43E-06
vg0718886562 sf0718885569 7 18886562 1.45E-09 8.54E-06
vg0143242911 sf0143241867 1 43242911 3.43E-09 5.52E-07
vg0407630134 sf0407625401 4 7630134 2.38E-08 2.54E-08
vg1017280876 sf1017209649 10 17280876 5.08E-07 NA
vg1207844031 sf1207841437 12 7844031 9.10E-06 9.25E-07