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 mr1374 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
vg1020531763 sf1020460242 10 20531763 3.45E-09 8.18E-08
vg0220342715 sf0220336847 2 20342715 4.25E-09 3.21E-07
vg0726559146 sf0726558152 7 26559146 1.06E-08 1.92E-07
vg0805992743 sf0805991746 8 5992743 2.01E-08 1.18E-06
vg0801628860 sf0801627862 8 1628860 6.03E-08 1.08E-06
vg1213065934 sf1213063273 12 13065934 1.85E-07 4.07E-06
vg0221838070 sf0221832201 2 21838070 1.99E-07 3.77E-06
vg0102103204 sf0102102204 1 2103204 4.18E-07 2.42E-06
vg0608005440 sf0608004441 6 8005440 4.74E-07 2.12E-06
vg0223525077 sf0223519208 2 23525077 5.21E-07 2.80E-06
vg0607755458 sf0607754459 6 7755458 4.01E-06 1.48E-06
vg0607659813 sf0607658814 6 7659813 5.91E-06 9.25E-07
vg0516508609 sf0516451091 5 16508609 6.77E-06 2.62E-06
vg0817557507 sf0817554793 8 17557507 7.81E-06 4.46E-06