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 mr1416 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
vg0717363054 sf0717362061 7 17363054 6.34E-26 NA
vg0703278160 sf0703277161 7 3278160 2.51E-25 NA
vg0707490731 sf0707489736 7 7490731 4.45E-25 NA
vg0205647907 sf0205647907 2 5647907 5.92E-25 NA
vg0428413031 sf0428227886 4 28413031 1.12E-24 NA
vg0138386033 sf0138384990 1 38386033 1.30E-22 1.00E-06
vg1202108841 sf1202107839 12 2108841 NA 8.26E-07
vg0420700412 sf0420528455 4 20700412 NA 8.96E-07
vg0709789120 sf0709788126 7 9789120 NA 4.13E-06