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 mr1788 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
vg1217929894 sf1217901328 12 17929894 6.06E-09 2.27E-06
vg0323847195 sf0323845369 3 23847195 6.83E-09 5.34E-06
vg0431915066 sf0431729961 4 31915066 4.92E-08 3.52E-06
vg0117290822 sf0117289776 1 17290822 3.07E-07 2.42E-06
vg0110800593 sf0110799569 1 10800593 4.53E-07 7.02E-07
vg1100795910 sf1100794911 11 795910 3.52E-06 2.26E-06
vg0316985667 sf0316984541 3 16985667 3.95E-06 5.04E-07
vg1119868109 sf1119402032 11 19868109 8.34E-06 NA
vg0431520593 sf0431335492 4 31520593 8.47E-06 NA
vg1217900467 sf1217871901 12 17900467 NA 2.52E-06
vg0142802503 sf0142801459 1 42802503 NA 4.67E-06
vg0622302006 sf0622301009 6 22302006 NA 7.32E-06