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 mr1853 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
vg0726399988 sf0726398994 7 26399988 1.28E-19 3.03E-08
vg0726430587 sf0726429593 7 26430587 4.99E-19 1.89E-08
vg0204440287 sf0204440284 2 4440287 8.62E-16 NA
vg1019763553 sf1019692053 10 19763553 1.76E-15 NA
vg1004334776 sf1004351314 10 4334776 2.15E-15 NA
vg0310762397 sf0310761313 3 10762397 2.77E-15 NA
vg1004352698 sf1004369236 10 4352698 3.47E-15 1.67E-06
vg1004482065 sf1004498603 10 4482065 2.98E-13 8.03E-07
vg1004256106 sf1004272644 10 4256106 NA 2.45E-07
vg1004262486 sf1004279024 10 4262486 NA 5.98E-07
vg1213118008 sf1213115347 12 13118008 NA 1.12E-06
vg1004572556 sf1004589094 10 4572556 NA 1.14E-06
vg1004782103 sf1004798640 10 4782103 NA 1.90E-06
vg1213849371 sf1213846709 12 13849371 NA 6.07E-06