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 mr1651 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
vg0709448532 sf0709447538 7 9448532 6.56E-08 6.56E-08
vg0626149778 sf0626148781 6 26149778 4.46E-07 4.46E-07
vg0704732672 sf0704731673 7 4732672 4.48E-07 4.48E-07
vg0714179494 sf0714178501 7 14179494 4.70E-07 4.70E-07
vg0202014334 sf0202014334 2 2014334 1.46E-06 1.46E-06
vg0420711795 sf0420539838 4 20711795 2.38E-06 2.38E-06
vg0709176903 sf0709175909 7 9176903 2.96E-06 2.96E-06
vg0621838550 sf0621837553 6 21838550 3.28E-06 3.28E-06
vg0612179300 sf0612178301 6 12179300 3.69E-06 3.70E-06
vg0717352217 sf0717351224 7 17352217 4.17E-06 4.17E-06