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 mr1626 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
vg0405531572 sf0405527013 4 5531572 8.86E-12 4.55E-10
vg0405270276 sf0405265717 4 5270276 4.52E-10 6.42E-07
vg0423976382 sf0423791240 4 23976382 1.89E-08 NA
vg0501424855 sf0501424839 5 1424855 2.63E-08 5.70E-06
vg0427602070 sf0427416931 4 27602070 8.15E-08 NA
vg0406863298 sf0406858743 4 6863298 2.10E-07 2.65E-06
vg0615097742 sf0615096743 6 15097742 2.27E-07 1.70E-06
vg0101292923 sf0101291923 1 1292923 3.78E-07 NA
vg0405302070 sf0405297511 4 5302070 4.45E-07 4.39E-06
vg0405990141 sf0405985581 4 5990141 6.03E-07 4.39E-06
vg1208509487 sf1208506894 12 8509487 1.80E-06 3.12E-06
vg1200826014 sf1200825014 12 826014 1.95E-06 2.25E-06
vg1222302867 sf1222269414 12 22302867 2.04E-06 2.71E-06
vg1215431363 sf1215428661 12 15431363 3.04E-06 4.62E-06
vg1200849729 sf1200848729 12 849729 4.41E-06 1.40E-06
vg0501009822 sf0501009805 5 1009822 8.15E-06 9.73E-06
vg0404027324 sf0404022931 4 4027324 NA 1.87E-06
vg1205810984 sf1205809966 12 5810984 NA 4.64E-06