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 mr1445 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
vg0403140954 sf0403136557 4 3140954 1.10E-07 2.40E-07
vg0826647662 sf0826644948 8 26647662 1.63E-07 3.33E-06
vg1103068554 sf1103064458 11 3068554 3.95E-07 NA
vg0709448532 sf0709447538 7 9448532 4.65E-07 1.35E-06
vg0629854146 sf0629853148 6 29854146 8.16E-07 1.97E-06
vg0712843936 sf0712842943 7 12843936 1.19E-06 1.40E-06
vg0521872068 sf0521809510 5 21872068 1.44E-06 3.63E-06
vg0517754242 sf0517693883 5 17754242 1.87E-06 4.21E-06
vg0921004343 sf0921003862 9 21004343 3.48E-06 NA
vg0626149778 sf0626148781 6 26149778 3.62E-06 2.94E-06
vg0621838550 sf0621837553 6 21838550 9.09E-06 3.16E-06