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 mr1910 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
vg1224058121 sf1224024575 12 24058121 4.08E-10 NA
vg1208281892 sf1208279298 12 8281892 1.09E-09 1.91E-06
vg0910262904 sf0910261903 9 10262904 1.57E-09 NA
vg1213457856 sf1213455194 12 13457856 1.96E-09 NA
vg0335186610 sf0335179479 3 35186610 2.18E-09 NA
vg1208436651 sf1208434058 12 8436651 2.36E-09 1.43E-06
vg1208281275 sf1208278681 12 8281275 2.03E-08 1.44E-06
vg0525794122 sf0525731543 5 25794122 4.54E-08 3.82E-06
vg0501163390 sf0501163374 5 1163390 1.02E-07 NA
vg0907980770 sf0907979770 9 7980770 1.36E-06 NA
vg0614105710 sf0614104711 6 14105710 NA 2.09E-06