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 mr1869 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
vg1213717963 sf1213715301 12 13717963 6.11E-08 6.11E-08
vg1213717956 sf1213715294 12 13717956 1.16E-07 1.16E-07
vg1102677343 sf1102673247 11 2677343 4.19E-07 4.19E-07
vg0223262220 sf0223256351 2 23262220 6.35E-07 6.36E-07
vg1214784988 sf1214782329 12 14784988 9.09E-07 9.09E-07
vg0217857667 sf0217851798 2 17857667 1.09E-06 1.09E-06
vg0418087588 sf0417915629 4 18087588 2.15E-06 2.16E-06
vg1214989214 sf1214986556 12 14989214 2.52E-06 2.52E-06
vg0914907851 sf0914906850 9 14907851 4.51E-06 4.51E-06
vg0416689969 sf0416518012 4 16689969 4.89E-06 4.90E-06