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 mr1632 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
vg0506847525 sf0506847467 5 6847525 2.18E-49 9.70E-35
vg0506871793 sf0506871735 5 6871793 3.72E-49 6.38E-35
vg1009363288 sf1009292109 10 9363288 5.91E-23 4.36E-10
vg1009362967 sf1009291788 10 9362967 6.13E-23 7.59E-12
vg0510448104 sf0510448033 5 10448104 4.21E-22 4.26E-14
vg1213203956 sf1213201294 12 13203956 6.14E-22 7.68E-16
vg0513464420 sf0513406967 5 13464420 1.71E-21 4.99E-14
vg1001247140 sf1001246117 10 1247140 8.03E-21 8.87E-10
vg0509447947 sf0509447876 5 9447947 9.67E-20 2.26E-12
vg0512420077 sf0512420007 5 12420077 1.85E-19 5.67E-15
vg0412231824 sf0412222535 4 12231824 1.19E-17 1.99E-09
vg0506869268 sf0506869210 5 6869268 6.14E-17 1.78E-14
vg0506936871 sf0506936813 5 6936871 1.19E-16 1.39E-12
vg0506104260 sf0506104199 5 6104260 9.75E-16 2.11E-08
vg1002265718 sf1002264695 10 2265718 3.85E-15 1.79E-07
vg0516212300 sf0516154782 5 16212300 1.54E-14 2.68E-08
vg0506633865 sf0506633806 5 6633865 2.24E-14 1.62E-09
vg0506577678 sf0506577619 5 6577678 5.94E-14 2.61E-08
vg0507847236 sf0507847177 5 7847236 1.16E-11 8.92E-10
vg0233906724 sf0233900855 2 33906724 1.23E-11 2.20E-08
vg0514650516 sf0514593059 5 14650516 3.31E-11 3.81E-10
vg0507628936 sf0507628877 5 7628936 2.65E-08 2.69E-07
vg0308719967 sf0308718905 3 8719967 9.43E-08 1.16E-07
vg0507253850 sf0507253792 5 7253850 1.23E-06 6.59E-08
vg0519672780 sf0519610264 5 19672780 NA 2.85E-07
vg0614104820 sf0614103821 6 14104820 NA 4.11E-06