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 mr1557 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
vg0918923523 sf0918922523 9 18923523 2.00E-41 1.10E-18
vg0301663427 sf0301662423 3 1663427 5.88E-32 8.78E-06
vg0208153831 sf0208153830 2 8153831 1.59E-31 6.28E-06
vg1219845789 sf1219817259 12 19845789 6.96E-27 NA
vg0308662136 sf0308661074 3 8662136 2.22E-25 NA
vg0918692246 sf0918691245 9 18692246 2.68E-24 2.06E-16
vg0917887843 sf0917886842 9 17887843 1.07E-17 6.60E-08
vg0207688311 sf0207688311 2 7688311 3.95E-17 3.35E-07
vg0918923624 sf0918922624 9 18923624 NA 3.24E-23
vg0918646540 sf0918645539 9 18646540 NA 4.11E-09
vg0918998633 sf0918997633 9 18998633 NA 7.62E-07
vg0918374002 sf0918373001 9 18374002 NA 1.80E-06
vg0919274820 sf0919274410 9 19274820 NA 3.42E-06