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 mr1182 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
vg0803653778 sf0803652781 8 3653778 9.35E-13 9.28E-09
vg0803656534 sf0803655537 8 3656534 2.04E-12 7.24E-09
vg0134272325 sf0134271282 1 34272325 1.99E-10 3.03E-07
vg0626321316 sf0626320319 6 26321316 3.69E-10 NA
vg0401346827 sf0401342377 4 1346827 4.36E-10 2.55E-06
vg0810146037 sf0810145041 8 10146037 6.91E-10 NA
vg0137195833 sf0137194790 1 37195833 2.76E-09 3.37E-06
vg1226678487 sf1226644883 12 26678487 2.14E-08 2.83E-06
vg0711760152 sf0711759158 7 11760152 5.60E-08 3.54E-06
vg1117453139 sf1116986994 11 17453139 NA 2.67E-06