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 mr1567 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
vg0724526928 sf0724525934 7 24526928 6.33E-23 3.28E-18
vg0724526921 sf0724525927 7 24526921 5.04E-22 1.34E-17
vg0701480178 sf0701479178 7 1480178 7.63E-14 2.99E-07
vg0103093065 sf0103092065 1 3093065 1.01E-13 2.78E-06
vg0724510628 sf0724509634 7 24510628 1.92E-12 1.04E-06
vg0102555772 sf0102554772 1 2555772 3.88E-12 9.89E-09
vg0235049174 sf0235043305 2 35049174 7.68E-12 NA
vg0724360759 sf0724359765 7 24360759 5.92E-09 2.30E-06
vg0724512350 sf0724511356 7 24512350 1.25E-08 4.70E-12
vg0528027144 sf0527964499 5 28027144 1.70E-08 6.59E-08
vg0724438382 sf0724437388 7 24438382 NA 4.20E-09
vg0620801911 sf0620800914 6 20801911 NA 4.93E-09
vg0724401667 sf0724400673 7 24401667 NA 2.89E-08
vg1106870375 sf1106866120 11 6870375 NA 1.39E-07
vg0317205386 sf0317204196 3 17205386 NA 5.24E-07
vg0316269128 sf0316267775 3 16269128 NA 7.33E-07
vg0203000556 sf0203000554 2 3000556 NA 8.85E-07
vg0804590579 sf0804589582 8 4590579 NA 1.06E-06
vg0607961607 sf0607960608 6 7961607 NA 1.57E-06
vg0918876795 sf0918875795 9 18876795 NA 2.52E-06
vg0314727656 sf0314726343 3 14727656 NA 4.80E-06
vg0317442397 sf0317441179 3 17442397 NA 8.13E-06
vg0316251221 sf0316249869 3 16251221 NA 8.40E-06