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 mr1024 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
vg0121172559 sf0121171514 1 21172559 8.34E-14 8.34E-14
vg0200274146 sf0200274146 2 274146 8.92E-12 8.92E-12
vg0127269769 sf0127268725 1 27269769 2.55E-10 2.55E-10
vg0507826953 sf0507826894 5 7826953 4.69E-10 4.69E-10
vg0335027666 sf0335020536 3 35027666 9.29E-10 9.29E-10
vg1215125172 sf1215122508 12 15125172 1.30E-09 1.30E-09
vg0826091106 sf0826088392 8 26091106 2.54E-09 2.54E-09
vg1014511015 sf1014439781 10 14511015 1.05E-08 1.05E-08
vg0102330722 sf0102329722 1 2330722 1.37E-08 1.37E-08
vg0919039056 sf0919038056 9 19039056 2.09E-08 2.09E-08
vg1211548501 sf1211545837 12 11548501 2.64E-08 2.64E-08
vg0426817741 sf0426632617 4 26817741 3.80E-08 3.80E-08
vg0139109454 sf0139108411 1 39109454 4.21E-08 4.21E-08
vg0434580936 sf0434395828 4 34580936 6.66E-08 6.66E-08
vg1227357675 sf1227324075 12 27357675 7.40E-08 7.40E-08
vg0124484350 sf0124483306 1 24484350 9.45E-08 9.45E-08
vg0620867473 sf0620866476 6 20867473 9.84E-08 9.83E-08
vg0623784364 sf0623783367 6 23784364 1.30E-07 1.30E-07
vg0114358681 sf0114357655 1 14358681 2.35E-07 2.35E-07
vg0107554036 sf0107553036 1 7554036 2.54E-07 2.54E-07