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 mr1011 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
vg1000348900 sf1000347900 10 348900 1.51E-08 1.51E-08
vg0304130869 sf0304129871 3 4130869 2.71E-07 2.71E-07
vg1213122631 sf1213119969 12 13122631 5.05E-07 5.05E-07
vg0304182141 sf0304181143 3 4182141 5.29E-07 5.30E-07
vg0310513352 sf0310512268 3 10513352 6.77E-07 6.77E-07
vg0120412875 sf0120411830 1 20412875 9.06E-07 9.07E-07
vg0139415631 sf0139414588 1 39415631 9.38E-07 9.38E-07
vg0610114031 sf0610113032 6 10114031 1.15E-06 1.15E-06
vg0625665252 sf0625664255 6 25665252 1.93E-06 1.93E-06
vg0803405756 sf0803404759 8 3405756 2.22E-06 2.22E-06
vg0807910368 sf0807909372 8 7910368 2.77E-06 2.77E-06
vg0139202994 sf0139201951 1 39202994 2.83E-06 2.83E-06
vg0307479900 sf0307478838 3 7479900 2.84E-06 2.84E-06
vg0314847905 sf0314846552 3 14847905 3.06E-06 3.06E-06
vg0616238331 sf0616237333 6 16238331 4.67E-06 4.67E-06