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 mr1538 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
vg0137855094 sf0137854051 1 37855094 8.63E-25 2.82E-17
vg0107015964 sf0107014964 1 7015964 4.04E-13 3.23E-08
vg1124043769 sf1123577639 11 24043769 6.93E-11 NA
vg1108505992 sf1108500602 11 8505992 8.46E-11 NA
vg0211863144 sf0211863140 2 11863144 1.23E-10 4.13E-06
vg0135573733 sf0135572690 1 35573733 2.44E-09 1.94E-07
vg0727484366 sf0727483372 7 27484366 2.74E-09 2.15E-08
vg0600574421 sf0600573422 6 574421 6.05E-09 1.53E-07
vg1127000154 sf1126528541 11 27000154 2.36E-08 1.52E-08
vg1208597833 sf1208595240 12 8597833 NA 3.36E-06
vg0816083361 sf0816080647 8 16083361 NA 4.77E-06