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 mr1717 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
vg0915452616 sf0915451615 9 15452616 7.45E-13 2.43E-06
vg0232092446 sf0232086577 2 32092446 2.27E-11 4.99E-06
vg0609807424 sf0609806425 6 9807424 4.54E-10 NA
vg0201029471 sf0201029471 2 1029471 4.55E-10 NA
vg0612902521 sf0612901522 6 12902521 6.06E-10 NA
vg1119381446 sf1118915134 11 19381446 NA 2.32E-07
vg0207123792 sf0207123792 2 7123792 NA 2.26E-06
vg1108224521 sf1108219131 11 8224521 NA 3.35E-06
vg0221016618 sf0221010750 2 21016618 NA 4.17E-06