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 mr1376 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
vg0306112666 sf0306111666 3 6112666 3.00E-09 4.61E-06
vg1007764381 sf1007779991 10 7764381 1.19E-08 6.04E-08
vg0723222806 sf0723221813 7 23222806 1.63E-08 6.39E-06
vg1127176280 sf1126704667 11 27176280 1.95E-08 1.05E-07
vg0723266585 sf0723265592 7 23266585 3.19E-08 6.47E-06
vg0722504993 sf0722504000 7 22504993 5.34E-08 3.81E-06
vg1126981238 sf1126509625 11 26981238 6.34E-08 3.40E-06
vg0707015142 sf0707014147 7 7015142 2.00E-06 2.59E-06
vg1208774960 sf1208772367 12 8774960 NA 3.28E-06