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 mr1386 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
vg0412534399 sf0412525109 4 12534399 2.62E-17 NA
vg0725709823 sf0725708829 7 25709823 1.19E-16 3.20E-07
vg0328057363 sf0328050417 3 28057363 5.41E-16 NA
vg0322708389 sf0322706878 3 22708389 8.13E-16 NA
vg0130417496 sf0130416452 1 30417496 1.05E-15 NA
vg1001165595 sf1001164571 10 1165595 6.38E-13 1.27E-06
vg0325099508 sf0325097589 3 25099508 4.65E-12 3.72E-06
vg1213206439 sf1213203777 12 13206439 NA 8.79E-07
vg1001405425 sf1001404402 10 1405425 NA 1.31E-06
vg0230180308 sf0230174439 2 30180308 NA 1.59E-06
vg1001165490 sf1001164466 10 1165490 NA 2.06E-06
vg1111678675 sf1111672992 11 11678675 NA 2.24E-06
vg0412229714 sf0412220425 4 12229714 NA 2.44E-06
vg0412409796 sf0412400511 4 12409796 NA 2.54E-06
vg0609249772 sf0609248773 6 9249772 NA 4.85E-06