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 mr1182 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
vg0803654150 sf0803653153 8 3654150 4.81E-20 6.86E-12
vg0724248089 sf0724247095 7 24248089 2.24E-18 8.58E-08
vg0401968013 sf0401963609 4 1968013 9.77E-18 1.55E-08
vg0401900537 sf0401896133 4 1900537 6.80E-17 1.36E-08
vg0137195833 sf0137194790 1 37195833 8.17E-17 1.10E-08
vg0618798718 sf0618797721 6 18798718 1.09E-16 5.14E-09
vg0626321316 sf0626320319 6 26321316 1.46E-16 1.76E-07
vg0917104880 sf0917103879 9 17104880 3.01E-16 3.41E-06
vg0919855604 sf0919855123 9 19855604 4.05E-16 6.18E-07
vg0604882288 sf0604881289 6 4882288 8.29E-16 4.94E-07
vg0134272325 sf0134271282 1 34272325 1.03E-15 2.71E-09
vg0405387818 sf0405383259 4 5387818 1.25E-15 3.65E-06
vg0612100813 sf0612099814 6 12100813 2.92E-15 8.60E-07
vg0409634255 sf0409624953 4 9634255 3.38E-15 2.63E-06
vg0113480569 sf0113479543 1 13480569 1.11E-14 2.21E-06
vg0810145390 sf0810144394 8 10145390 1.26E-14 1.11E-06
vg0427120618 sf0426935488 4 27120618 5.48E-14 4.65E-06
vg1209042641 sf1209040050 12 9042641 9.97E-14 2.17E-06
vg0401227972 sf0401223522 4 1227972 4.69E-12 1.43E-06
vg0618517700 sf0618516703 6 18517700 3.82E-11 1.89E-07
vg0803658896 sf0803657899 8 3658896 NA 9.83E-10
vg0622510569 sf0622509572 6 22510569 NA 3.29E-07
vg0621761253 sf0621760256 6 21761253 NA 8.27E-07
vg0106645732 sf0106644732 1 6645732 NA 2.43E-06
vg1105347465 sf1105343216 11 5347465 NA 5.64E-06