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 mr1768 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
vg0719153511 sf0719152518 7 19153511 7.92E-09 2.16E-07
vg0122694254 sf0122693209 1 22694254 3.33E-08 5.67E-07
vg0818948966 sf0818946253 8 18948966 3.94E-08 7.80E-07
vg0717366548 sf0717365555 7 17366548 6.28E-08 1.74E-06
vg1003004399 sf1003003376 10 3004399 1.27E-07 1.23E-07
vg0906086651 sf0906085651 9 6086651 1.27E-07 4.98E-07
vg1217949062 sf1217920496 12 17949062 1.41E-07 1.23E-06
vg1010550381 sf1010479202 10 10550381 1.72E-07 1.47E-06
vg1010554538 sf1010483359 10 10554538 1.75E-07 2.69E-07
vg1004963171 sf1004979708 10 4963171 1.79E-07 1.34E-06
vg1010265724 sf1010194545 10 10265724 1.89E-07 2.30E-06
vg0715690956 sf0715689963 7 15690956 2.05E-07 2.16E-06
vg1007003848 sf1007019471 10 7003848 3.62E-07 1.07E-06
vg0432212716 sf0432027608 4 32212716 3.63E-07 3.33E-07
vg0101350174 sf0101349174 1 1350174 3.74E-07 2.31E-06
vg1003193153 sf1003192130 10 3193153 4.03E-07 5.34E-07
vg0507345057 sf0507344999 5 7345057 4.20E-07 2.16E-06
vg0819864400 sf0819861687 8 19864400 4.58E-07 1.60E-06
vg1003382071 sf1003381048 10 3382071 1.08E-06 8.53E-07
vg0412792771 sf0412783481 4 12792771 1.43E-06 1.10E-06
vg0715368259 sf0715367266 7 15368259 6.44E-06 NA