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 mr1242 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
vg0222693356 sf0222687487 2 22693356 1.86E-48 1.54E-26
vg1110425815 sf1110420360 11 10425815 2.23E-27 1.37E-10
vg0505887711 sf0505887649 5 5887711 2.35E-25 7.32E-08
vg0316096221 sf0316094868 3 16096221 9.26E-25 2.42E-08
vg0112313831 sf0112312805 1 12313831 1.89E-24 1.97E-06
vg1218624984 sf1218596420 12 18624984 2.22E-24 3.54E-09
vg0335906768 sf0335899637 3 35906768 4.07E-24 1.48E-09
vg0818228918 sf0818226205 8 18228918 1.99E-23 1.80E-08
vg0311969153 sf0311967871 3 11969153 7.07E-23 3.22E-08
vg0316147114 sf0316145761 3 16147114 1.25E-22 6.60E-09
vg1204550069 sf1204549057 12 4550069 3.65E-22 4.07E-08
vg0314739384 sf0314738071 3 14739384 4.01E-22 8.12E-09
vg0501379198 sf0501379182 5 1379198 7.44E-22 6.55E-09
vg0528516881 sf0528454236 5 28516881 8.91E-22 2.68E-09
vg0907026290 sf0907025290 9 7026290 3.24E-21 1.06E-08
vg0805989476 sf0805988479 8 5989476 1.13E-19 1.33E-07
vg0434845674 sf0434660565 4 34845674 1.36E-18 1.68E-06
vg0222722554 sf0222716685 2 22722554 NA 1.34E-15
vg0222948971 sf0222943102 2 22948971 NA 1.02E-09
vg0222696182 sf0222690313 2 22696182 NA 5.71E-09
vg0626215270 sf0626214273 6 26215270 NA 6.54E-09
vg0327037726 sf0327030779 3 27037726 NA 1.03E-08
vg0129623631 sf0129622586 1 29623631 NA 1.23E-08
vg1218466305 sf1218437741 12 18466305 NA 1.33E-08
vg0232374274 sf0232368405 2 32374274 NA 5.56E-08
vg1016363154 sf1016291930 10 16363154 NA 1.95E-07
vg0505523915 sf0505523853 5 5523915 NA 6.25E-06