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 mr1577 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
vg0804751253 sf0804750256 8 4751253 2.49E-10 NA
vg1210574208 sf1210571621 12 10574208 1.22E-09 NA
vg1215959584 sf1215956880 12 15959584 1.99E-09 NA
vg1210023832 sf1210021243 12 10023832 3.97E-09 4.98E-07
vg1215706891 sf1215704188 12 15706891 5.63E-09 4.93E-07
vg1210023864 sf1210021275 12 10023864 5.84E-09 3.33E-07
vg1120489837 sf1120023762 11 20489837 6.69E-09 6.80E-07
vg0805619517 sf0805618520 8 5619517 9.09E-09 1.57E-06
vg0318167000 sf0318165782 3 18167000 1.22E-08 2.39E-06
vg0122939348 sf0122938304 1 22939348 1.16E-07 1.04E-07
vg0503490446 sf0503490423 5 3490446 1.98E-06 4.68E-06
vg0218703489 sf0218697620 2 18703489 2.55E-06 NA
vg0503485496 sf0503485473 5 3485496 3.62E-06 7.20E-06