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 mr1388 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
vg1214120671 sf1214118011 12 14120671 3.96E-08 3.10E-07
vg0431634180 sf0431449073 4 31634180 7.55E-08 NA
vg0820513390 sf0820510677 8 20513390 8.18E-08 1.87E-06
vg0820890632 sf0820887919 8 20890632 8.85E-08 NA
vg0119598439 sf0119597394 1 19598439 1.54E-07 NA
vg0718838390 sf0718837397 7 18838390 1.74E-07 2.93E-07
vg0207179503 sf0207179503 2 7179503 4.40E-07 1.53E-06
vg0911580904 sf0911579903 9 11580904 4.65E-07 1.57E-06
vg0820512665 sf0820509952 8 20512665 5.45E-07 3.22E-06
vg0911764924 sf0911763923 9 11764924 5.20E-06 2.93E-06
vg0600083785 sf0600082785 6 83785 NA 5.05E-06