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 mr1860 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
vg0918158744 sf0918157743 9 18158744 2.00E-17 1.12E-10
vg0916242445 sf0916241444 9 16242445 8.14E-17 5.16E-11
vg0916209370 sf0916208369 9 16209370 1.78E-13 2.36E-07
vg0918447666 sf0918446665 9 18447666 7.81E-12 1.39E-06
vg0611557966 sf0611556967 6 11557966 1.30E-10 6.60E-07
vg0919157155 sf0919156744 9 19157155 3.43E-10 NA
vg0611558643 sf0611557644 6 11558643 4.57E-10 1.79E-06
vg0140618344 sf0140617301 1 40618344 4.85E-10 4.96E-06
vg0611577935 sf0611576936 6 11577935 9.35E-09 2.83E-06
vg0216477558 sf0216471688 2 16477558 1.05E-06 3.18E-06
vg0507006230 sf0507006172 5 7006230 8.62E-06 NA