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 mr1716 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
vg1017087028 sf1017015800 10 17087028 3.80E-13 3.47E-07
vg0113584886 sf0113583860 1 13584886 1.12E-10 NA
vg0710292737 sf0710291743 7 10292737 1.80E-10 7.14E-06
vg0400075143 sf0400074143 4 75143 1.82E-10 NA
vg0520084429 sf0520021905 5 20084429 2.67E-10 NA
vg0520041393 sf0519978869 5 20041393 7.76E-10 4.78E-07
vg0729692653 sf0729691661 7 29692653 2.29E-09 3.41E-06
vg0409022880 sf0409018155 4 9022880 1.59E-08 2.50E-06
vg1222304933 sf1222271480 12 22304933 5.61E-08 2.83E-06
vg0408053796 sf0408049068 4 8053796 1.60E-07 NA
vg1017039650 sf1016968422 10 17039650 NA 2.00E-06
vg1218169348 sf1218140784 12 18169348 NA 2.44E-06