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 mr1004 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
vg0715019955 sf0715018962 7 15019955 2.36E-08 2.36E-08
vg0229842767 sf0229836898 2 29842767 1.35E-07 1.35E-07
vg0336013947 sf0336006816 3 36013947 2.22E-07 2.22E-07
vg0229815178 sf0229809309 2 29815178 3.36E-07 3.36E-07
vg0807248488 sf0807247493 8 7248488 7.94E-07 7.95E-07
vg0336037583 sf0336030452 3 36037583 8.76E-07 8.76E-07
vg0303782877 sf0303781873 3 3782877 1.10E-06 1.10E-06
vg0708138138 sf0708137143 7 8138138 1.14E-06 1.14E-06
vg1217448754 sf1217442709 12 17448754 1.20E-06 1.20E-06
vg0627259502 sf0627258505 6 27259502 1.49E-06 1.49E-06
vg0916644408 sf0916643407 9 16644408 2.05E-06 2.05E-06
vg0820509533 sf0820506820 8 20509533 2.20E-06 2.20E-06
vg0234915674 sf0234909805 2 34915674 2.57E-06 2.57E-06
vg0431577231 sf0431392127 4 31577231 2.69E-06 2.69E-06
vg0715958325 sf0715957332 7 15958325 2.98E-06 2.98E-06
vg0419950118 sf0419778154 4 19950118 3.04E-06 3.04E-06
vg0715495349 sf0715494356 7 15495349 4.23E-06 4.23E-06
vg0103416985 sf0103415985 1 3416985 4.31E-06 4.31E-06