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 mr1715 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
vg0235121354 sf0235115485 2 35121354 1.19E-10 NA
vg0706614349 sf0706613354 7 6614349 3.77E-10 NA
vg0401161192 sf0401156742 4 1161192 6.29E-10 NA
vg0623192526 sf0623191529 6 23192526 3.92E-09 NA
vg0125066238 sf0125065194 1 25066238 5.37E-09 NA
vg0401709977 sf0401705526 4 1709977 2.71E-07 NA
vg0402529380 sf0402524985 4 2529380 3.79E-07 3.01E-06
vg0404000463 sf0403996070 4 4000463 7.06E-07 NA
vg0218733532 sf0218727663 2 18733532 7.71E-07 NA
vg0519440425 sf0519377909 5 19440425 1.35E-06 NA
vg0810981948 sf0810980953 8 10981948 8.02E-06 NA
vg0529835448 sf0529772803 5 29835448 NA 1.88E-06
vg1218169215 sf1218140651 12 18169215 NA 3.08E-06