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 mr1803 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
vg0805576605 sf0805575608 8 5576605 1.44E-18 NA
vg0124234050 sf0124233006 1 24234050 5.07E-17 NA
vg0920168243 sf0920167762 9 20168243 9.93E-17 NA
vg0422485909 sf0422300796 4 22485909 1.11E-16 NA
vg0302722497 sf0302721493 3 2722497 1.34E-16 NA
vg0124389643 sf0124388599 1 24389643 2.27E-13 NA
vg1210596771 sf1210594184 12 10596771 9.40E-13 7.41E-07
vg1215558096 sf1215555393 12 15558096 NA 1.15E-08
vg0122939348 sf0122938304 1 22939348 NA 2.25E-08
vg1210023864 sf1210021275 12 10023864 NA 4.74E-07
vg0318167000 sf0318165782 3 18167000 NA 1.28E-06
vg0503490446 sf0503490423 5 3490446 NA 3.23E-06
vg0503485496 sf0503485473 5 3485496 NA 3.63E-06
vg1120997358 sf1120531237 11 20997358 NA 3.91E-06