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 mr1118 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
vg0222673217 sf0222667348 2 22673217 1.03E-30 3.49E-24
vg1009101162 sf1009030023 10 9101162 2.79E-30 2.04E-07
vg1007270851 sf1007286474 10 7270851 7.70E-28 3.67E-07
vg1005668884 sf1005685422 10 5668884 7.48E-26 NA
vg0407827227 sf0407822495 4 7827227 8.04E-26 NA
vg1007460164 sf1007475787 10 7460164 4.32E-25 7.91E-09
vg1007541601 sf1007557213 10 7541601 3.41E-21 6.24E-08
vg1223504725 sf1223471185 12 23504725 1.77E-18 3.45E-07
vg1009127352 sf1009056213 10 9127352 1.69E-17 1.84E-09
vg0121803138 sf0121802093 1 21803138 1.76E-17 3.84E-08
vg0222739148 sf0222733279 2 22739148 9.17E-17 6.79E-20
vg0235325400 sf0235319531 2 35325400 3.04E-16 2.23E-07
vg0221001490 sf0220995622 2 21001490 2.22E-15 NA
vg0222722554 sf0222716685 2 22722554 NA 2.48E-12
vg1007435905 sf1007451528 10 7435905 NA 1.89E-11
vg1007506160 sf1007521783 10 7506160 NA 2.47E-10
vg0616706040 sf0616705042 6 16706040 NA 5.79E-09
vg0905859096 sf0905858096 9 5859096 NA 1.44E-08
vg1110425815 sf1110420360 11 10425815 NA 1.83E-08
vg0141556686 sf0141555643 1 41556686 NA 3.26E-08
vg0141599747 sf0141598704 1 41599747 NA 7.66E-08
vg0222926098 sf0222920229 2 22926098 NA 7.74E-08
vg0306047262 sf0306046262 3 6047262 NA 1.19E-07
vg0518620627 sf0518558110 5 18620627 NA 1.63E-07
vg0327037726 sf0327030779 3 27037726 NA 1.74E-07
vg0222948971 sf0222943102 2 22948971 NA 1.95E-07
vg1016227917 sf1016156689 10 16227917 NA 2.03E-07
vg0222636576 sf0222630707 2 22636576 NA 2.21E-07
vg0709837237 sf0709836243 7 9837237 NA 3.14E-07
vg0316147114 sf0316145761 3 16147114 NA 3.35E-07
vg1118813179 sf1118346987 11 18813179 NA 4.26E-07