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 mr1771 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
vg1018563179 sf1018491736 10 18563179 4.87E-24 2.48E-08
vg1018583477 sf1018512034 10 18583477 2.01E-23 6.33E-09
vg0515920069 sf0515862576 5 15920069 2.56E-17 NA
vg1219997122 sf1219968564 12 19997122 2.75E-17 NA
vg0401787914 sf0401783510 4 1787914 3.27E-17 NA
vg0523062907 sf0523000348 5 23062907 6.80E-17 NA
vg1209876216 sf1209873626 12 9876216 NA 3.36E-07
vg0105393860 sf0105392860 1 5393860 NA 2.71E-06
vg1220092619 sf1220064061 12 20092619 NA 2.79E-06
vg1124416534 sf1123950374 11 24416534 NA 3.12E-06