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 mr1252 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
vg0402376506 sf0402372101 4 2376506 3.89E-12 8.96E-07
vg0234326223 sf0234320354 2 34326223 1.19E-11 3.10E-07
vg0524852282 sf0524789697 5 24852282 2.88E-11 6.19E-06
vg0432953400 sf0432768287 4 32953400 1.21E-10 9.55E-06
vg0115920715 sf0115919689 1 15920715 1.82E-10 NA
vg0203951429 sf0203951426 2 3951429 2.21E-09 NA
vg1210504546 sf1210501959 12 10504546 2.86E-09 2.40E-06
vg0520300536 sf0520238009 5 20300536 5.68E-07 NA
vg0316985667 sf0316984541 3 16985667 1.01E-06 1.57E-06
vg0714101037 sf0714100044 7 14101037 1.09E-06 NA
vg0630884821 sf0630883823 6 30884821 NA 1.36E-06
vg0130094621 sf0130093576 1 30094621 NA 4.80E-06