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 mr1028 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
vg0329856598 sf0329849637 3 29856598 3.73E-10 NA
vg0517778734 sf0517718220 5 17778734 6.63E-10 NA
vg0922565216 sf0922564735 9 22565216 7.90E-10 NA
vg0332498725 sf0332491598 3 32498725 8.40E-10 NA
vg0112046165 sf0112045139 1 12046165 9.60E-10 NA
vg0809969756 sf0809968760 8 9969756 8.26E-09 NA
vg1114869505 sf1114405819 11 14869505 1.55E-07 7.89E-06
vg0625085974 sf0625084977 6 25085974 7.73E-07 9.99E-07
vg0625011546 sf0625010549 6 25011546 8.43E-07 7.01E-07
vg0305993129 sf0305992129 3 5993129 1.96E-06 NA
vg1212988611 sf1212985950 12 12988611 2.37E-06 NA
vg1222877698 sf1222844138 12 22877698 NA 6.61E-07