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 mr1170 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
vg0206232457 sf0206232457 2 6232457 9.80E-21 3.03E-09
vg0708802081 sf0708801086 7 8802081 1.14E-17 NA
vg0800430481 sf0800429481 8 430481 8.43E-17 NA
vg0110176224 sf0110175200 1 10176224 1.74E-16 5.00E-06
vg0914141146 sf0914140145 9 14141146 2.73E-16 NA
vg1222944058 sf1222910517 12 22944058 2.07E-13 NA
vg0823352400 sf0823349687 8 23352400 2.86E-13 NA
vg0429286814 sf0429101676 4 29286814 2.40E-12 NA
vg1122458810 sf1121992681 11 22458810 3.57E-12 3.40E-06
vg0206038889 sf0206038889 2 6038889 NA 2.87E-07
vg0233523559 sf0233517690 2 33523559 NA 3.61E-06
vg1122503980 sf1122037851 11 22503980 NA 7.90E-06