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 mr1691 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
vg0304685909 sf0304684911 3 4685909 6.12E-14 2.09E-08
vg0225193157 sf0225187288 2 25193157 4.99E-12 4.87E-06
vg0107054597 sf0107053597 1 7054597 6.45E-12 6.81E-07
vg0519414866 sf0519352350 5 19414866 8.92E-12 NA
vg0804650293 sf0804649296 8 4650293 9.42E-12 9.97E-07
vg1015811222 sf1015739992 10 15811222 1.15E-11 2.17E-06
vg0624013853 sf0624012856 6 24013853 1.30E-10 1.32E-06
vg0107756494 sf0107755494 1 7756494 4.67E-10 3.31E-06
vg1001996513 sf1001995490 10 1996513 1.20E-09 3.13E-06
vg0401256003 sf0401251553 4 1256003 3.80E-09 6.59E-06
vg1204610850 sf1204609838 12 4610850 NA 3.51E-08
vg1204671441 sf1204670429 12 4671441 NA 8.61E-08
vg0134236787 sf0134235744 1 34236787 NA 4.57E-07
vg1218051198 sf1218022634 12 18051198 NA 5.90E-07
vg1121357584 sf1120891461 11 21357584 NA 1.57E-06
vg0134236950 sf0134235907 1 34236950 NA 2.62E-06
vg0140756777 sf0140755734 1 40756777 NA 3.92E-06
vg1204640879 sf1204639867 12 4640879 NA 4.74E-06