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 mr1879 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
vg1217053914 sf1217047868 12 17053914 1.11E-16 1.92E-08
vg1212888454 sf1212885793 12 12888454 1.60E-15 NA
vg0122872464 sf0122871420 1 22872464 3.97E-14 NA
vg1123212318 sf1122746189 11 23212318 7.88E-14 NA
vg0309453680 sf0309452616 3 9453680 1.12E-13 NA
vg0910781140 sf0910780139 9 10781140 2.57E-11 NA
vg0107647091 sf0107646091 1 7647091 3.81E-11 3.79E-09
vg0401348208 sf0401343758 4 1348208 NA 7.16E-07
vg1002941120 sf1002940097 10 2941120 NA 1.49E-06
vg0402081771 sf0402077365 4 2081771 NA 2.95E-06
vg0223519995 sf0223514126 2 23519995 NA 2.95E-06
vg0205031937 sf0205031934 2 5031937 NA 3.05E-06
vg0605321614 sf0605320615 6 5321614 NA 3.29E-06
vg0728490686 sf0728489694 7 28490686 NA 4.59E-06