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 mr1853 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
vg1212822297 sf1212819636 12 12822297 3.09E-18 5.13E-09
vg0315319895 sf0315318542 3 15319895 3.80E-16 6.90E-06
vg0726727372 sf0726726378 7 26727372 2.42E-15 NA
vg1216569725 sf1216567018 12 16569725 2.60E-15 NA
vg0420626346 sf0420454389 4 20626346 2.64E-15 NA
vg1004572365 sf1004588903 10 4572365 5.18E-12 6.27E-07
vg0213591886 sf0213591882 2 13591886 NA 3.38E-07
vg0413765723 sf0413756437 4 13765723 NA 8.93E-07
vg0413764976 sf0413755690 4 13764976 NA 2.92E-06
vg0228504159 sf0228498290 2 28504159 NA 4.59E-06