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 mr1587 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
vg0422485909 sf0422300796 4 22485909 2.65E-13 2.13E-06
vg1214830861 sf1214828202 12 14830861 1.00E-12 3.36E-09
vg1220906459 sf1220873008 12 20906459 1.29E-11 2.35E-06
vg0134320353 sf0134319310 1 34320353 2.69E-11 NA
vg1210413478 sf1210410891 12 10413478 1.65E-10 NA
vg0801293540 sf0801292542 8 1293540 2.89E-10 NA
vg0804871904 sf0804870907 8 4871904 4.21E-10 3.76E-06
vg1210130934 sf1210128345 12 10130934 5.38E-10 1.78E-06
vg0805771768 sf0805770771 8 5771768 4.44E-08 1.26E-06
vg1223873637 sf1223840090 12 23873637 6.68E-08 4.60E-06
vg0122959545 sf0122958501 1 22959545 3.15E-07 3.40E-06
vg1216321310 sf1216318606 12 16321310 6.58E-07 1.96E-06
vg0233855896 sf0233850027 2 33855896 NA 3.23E-07
vg0123622273 sf0123621229 1 23622273 NA 1.36E-06
vg0123622337 sf0123621293 1 23622337 NA 2.31E-06
vg0123559524 sf0123558480 1 23559524 NA 2.35E-06
vg1020743019 sf1020671498 10 20743019 NA 4.66E-06