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 mr1739 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
vg0316516166 sf0316514811 3 16516166 5.72E-09 3.89E-07
vg0400652453 sf0400651452 4 652453 1.25E-08 7.75E-06
vg1007607743 sf1007623352 10 7607743 1.33E-07 4.42E-06
vg0432999456 sf0432814342 4 32999456 1.97E-07 4.21E-06
vg0316166709 sf0316165356 3 16166709 3.06E-07 3.71E-07
vg0434375534 sf0434190428 4 34375534 1.29E-06 NA
vg1125768032 sf1125301871 11 25768032 NA 1.28E-06
vg0223262220 sf0223256351 2 23262220 NA 1.97E-06