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 mr1148 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
vg0222725881 sf0222720012 2 22725881 3.48E-30 2.72E-16
vg0222732157 sf0222726288 2 22732157 3.60E-30 1.35E-16
vg1223437952 sf1223404412 12 23437952 8.48E-19 NA
vg0710418364 sf0710417370 7 10418364 1.10E-18 NA
vg1219910283 sf1219881753 12 19910283 1.12E-18 NA
vg0721621489 sf0721620496 7 21621489 1.63E-18 NA
vg0130736176 sf0130735132 1 30736176 NA 9.25E-09
vg0222725003 sf0222719134 2 22725003 NA 1.51E-08
vg0130644853 sf0130643809 1 30644853 NA 2.43E-08
vg0105130764 sf0105129764 1 5130764 NA 3.29E-07
vg0335796573 sf0335789442 3 35796573 NA 1.90E-06
vg0101295924 sf0101294924 1 1295924 NA 2.55E-06
vg1116467363 sf1116002240 11 16467363 NA 2.67E-06
vg0322574715 sf0322573204 3 22574715 NA 3.07E-06
vg0205554770 sf0205554770 2 5554770 NA 3.08E-06
vg0223422615 sf0223416746 2 23422615 NA 4.31E-06
vg0335946674 sf0335939543 3 35946674 NA 4.91E-06