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 mr1657 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
vg0507948596 sf0507948537 5 7948596 2.05E-15 NA
vg0828040582 sf0828037868 8 28040582 2.26E-15 NA
vg1226040946 sf1226007340 12 26040946 3.94E-15 NA
vg0206625109 sf0206625109 2 6625109 2.23E-14 NA
vg0327474789 sf0327467842 3 27474789 2.38E-14 NA
vg0507940286 sf0507940227 5 7940286 6.47E-14 2.16E-06
vg0138071701 sf0138070658 1 38071701 9.10E-13 NA
vg0234501233 sf0234495364 2 34501233 2.34E-11 NA
vg0129279095 sf0129278050 1 29279095 NA 1.46E-07
vg0726456019 sf0726455025 7 26456019 NA 2.62E-06
vg0427439811 sf0427254675 4 27439811 NA 3.98E-06