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 mr1120 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
vg0421387824 sf0421215877 4 21387824 1.24E-12 1.81E-10
vg0421388196 sf0421216249 4 21388196 2.35E-11 5.14E-09
vg0224540597 sf0224534728 2 24540597 9.91E-10 2.90E-08
vg0728000317 sf0727999324 7 28000317 1.59E-09 7.18E-08
vg1217621842 sf1217615797 12 17621842 1.74E-09 6.13E-07
vg0504875404 sf0504875381 5 4875404 5.90E-09 4.20E-07
vg0700863821 sf0700862821 7 863821 6.52E-09 1.40E-06
vg0336193973 sf0336186899 3 36193973 1.23E-08 9.27E-07
vg1204723475 sf1204722460 12 4723475 1.48E-08 1.39E-06
vg0139756098 sf0139755055 1 39756098 4.49E-08 8.52E-07
vg0625443240 sf0625442243 6 25443240 5.79E-08 2.49E-06
vg1209218924 sf1209216333 12 9218924 6.24E-08 9.91E-07
vg0134943001 sf0134941958 1 34943001 7.77E-08 3.49E-06
vg0727091511 sf0727090517 7 27091511 8.83E-08 1.09E-06
vg1117137503 sf1116671355 11 17137503 9.76E-08 5.05E-07
vg1002009944 sf1002008921 10 2009944 2.80E-07 4.79E-06
vg0618348783 sf0618347786 6 18348783 3.49E-06 1.04E-06
vg0428087648 sf0427902514 4 28087648 NA 4.71E-06