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 mr1970 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
vg0607282803 sf0607281804 6 7282803 2.08E-107 3.44E-26
vg0428552129 sf0428366981 4 28552129 5.42E-77 NA
vg0717275313 sf0717274320 7 17275313 2.87E-74 NA
vg0501558999 sf0501558983 5 1558999 8.44E-74 NA
vg0917257825 sf0917256824 9 17257825 3.00E-73 NA
vg0607252722 sf0607251723 6 7252722 NA 2.61E-17
vg0607242219 sf0607241220 6 7242219 NA 1.07E-12
vg0123635868 sf0123634824 1 23635868 NA 1.30E-07
vg0607014877 sf0607013878 6 7014877 NA 2.46E-07
vg0500739274 sf0500739274 5 739274 NA 3.92E-07
vg1122051649 sf1121585520 11 22051649 NA 8.24E-07
vg0607310239 sf0607309240 6 7310239 NA 1.59E-06
vg0607383125 sf0607382126 6 7383125 NA 1.95E-06
vg0123559107 sf0123558063 1 23559107 NA 2.60E-06
vg0123426824 sf0123425780 1 23426824 NA 2.65E-06
vg0819150140 sf0819147427 8 19150140 NA 2.90E-06
vg1121911671 sf1121445542 11 21911671 NA 3.21E-06
vg0606972701 sf0606971702 6 6972701 NA 4.35E-06
vg0607385204 sf0607384205 6 7385204 NA 4.53E-06