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 mr1579 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
vg0726964336 sf0726963342 7 26964336 3.22E-21 NA
vg0104443530 sf0104442530 1 4443530 3.54E-19 NA
vg0421015426 sf0420843479 4 21015426 9.00E-19 NA
vg0826622371 sf0826619657 8 26622371 1.30E-18 NA
vg0718149327 sf0718148334 7 18149327 1.50E-18 NA
vg0214006862 sf0214000992 2 14006862 1.24E-14 NA
vg1124892966 sf1124426806 11 24892966 NA 8.10E-09
vg0912105870 sf0912104869 9 12105870 NA 1.24E-06
vg1124715978 sf1124249818 11 24715978 NA 1.27E-06
vg1122132197 sf1121666068 11 22132197 NA 3.06E-06
vg1110750346 sf1110744891 11 10750346 NA 9.36E-06
vg0907951531 sf0907950531 9 7951531 NA 9.70E-06