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 mr1602 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
vg1217943070 sf1217914504 12 17943070 3.70E-08 NA
vg0405137895 sf0405133337 4 5137895 7.44E-08 NA
vg1217404715 sf1217398670 12 17404715 1.22E-07 1.49E-06
vg0405116940 sf0405112382 4 5116940 3.80E-07 NA
vg0715275897 sf0715274904 7 15275897 1.91E-06 NA
vg1214507607 sf1214504948 12 14507607 6.19E-06 NA
vg1104313331 sf1104309233 11 4313331 9.61E-06 NA
vg0101299481 sf0101298481 1 1299481 NA 2.98E-06