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 mr1705 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
vg0716330932 sf0716329939 7 16330932 9.92E-13 4.50E-08
vg0412992801 sf0412983511 4 12992801 5.06E-11 2.38E-07
vg0716554113 sf0716553120 7 16554113 2.12E-10 2.57E-07
vg0205395417 sf0205395417 2 5395417 2.15E-10 4.02E-08
vg0413075261 sf0413065971 4 13075261 3.05E-10 2.25E-07
vg0317222689 sf0317221499 3 17222689 6.40E-10 7.17E-06
vg0431236819 sf0431051709 4 31236819 5.48E-09 3.71E-06
vg0334678225 sf0334671095 3 34678225 1.34E-08 1.95E-06
vg1004874392 sf1004890929 10 4874392 9.50E-08 1.43E-06
vg1207849594 sf1207847000 12 7849594 1.65E-06 NA
vg0117282717 sf0117281671 1 17282717 1.72E-06 3.36E-06
vg0107014942 sf0107013942 1 7014942 2.45E-06 NA