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 mr1521 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
vg0419251939 sf0419079977 4 19251939 5.65E-24 3.65E-10
vg0130660290 sf0130659246 1 30660290 6.71E-18 NA
vg0725742670 sf0725741676 7 25742670 2.26E-17 NA
vg0230082625 sf0230076756 2 30082625 4.47E-17 NA
vg1219149829 sf1219121263 12 19149829 8.09E-17 NA
vg0135640886 sf0135639843 1 35640886 4.57E-15 NA
vg0726140074 sf0726139080 7 26140074 NA 4.74E-08
vg0726131769 sf0726130775 7 26131769 NA 8.29E-08
vg0327524627 sf0327517680 3 27524627 NA 8.28E-07
vg0600858412 sf0600857413 6 858412 NA 1.17E-06
vg0419267605 sf0419095643 4 19267605 NA 2.32E-06
vg0220795440 sf0220789572 2 20795440 NA 3.66E-06
vg0402252645 sf0402248240 4 2252645 NA 4.55E-06
vg0816476794 sf0816474080 8 16476794 NA 4.98E-06
vg0213579772 sf0213579768 2 13579772 NA 9.05E-06