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 mr1016 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
vg1215955784 sf1215953080 12 15955784 9.71E-42 3.19E-22
vg1215967035 sf1215964331 12 15967035 2.49E-41 1.19E-22
vg1011511779 sf1011440598 10 11511779 1.92E-16 2.03E-06
vg1212877317 sf1212874656 12 12877317 8.63E-16 1.86E-06
vg0630798684 sf0630797686 6 30798684 2.31E-15 NA
vg1218663003 sf1218634438 12 18663003 5.19E-15 8.57E-10
vg0521485463 sf0521422904 5 21485463 9.48E-15 9.18E-07
vg1006587700 sf1006603323 10 6587700 5.39E-14 1.91E-09
vg1011512046 sf1011440865 10 11512046 1.76E-12 4.27E-09
vg1022588644 sf1022517118 10 22588644 3.41E-12 7.09E-11
vg0527788086 sf0527710773 5 27788086 9.81E-11 2.63E-06
vg1208048502 sf1208045908 12 8048502 1.50E-10 7.94E-07
vg1211633613 sf1211630949 12 11633613 2.96E-10 1.87E-06
vg1215870946 sf1215868242 12 15870946 NA 9.68E-13
vg1206197673 sf1206196564 12 6197673 NA 2.91E-07
vg1213186520 sf1213183858 12 13186520 NA 5.29E-07
vg0432161866 sf0431976759 4 32161866 NA 5.30E-07
vg0408293903 sf0408289177 4 8293903 NA 1.10E-06
vg0623791757 sf0623790760 6 23791757 NA 1.23E-06
vg0402261971 sf0402257566 4 2261971 NA 1.26E-06
vg1216828835 sf1216822789 12 16828835 NA 1.48E-06
vg0809365446 sf0809364450 8 9365446 NA 1.94E-06
vg0901555655 sf0901554655 9 1555655 NA 2.25E-06
vg0820168380 sf0820165667 8 20168380 NA 2.43E-06