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 mr1261 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
vg0726337284 sf0726336290 7 26337284 3.20E-08 3.20E-08
vg0114643712 sf0114642686 1 14643712 5.71E-08 5.72E-08
vg0723562063 sf0723561070 7 23562063 1.84E-07 1.84E-07
vg0721868538 sf0721867545 7 21868538 1.89E-07 1.89E-07
vg1005616181 sf1005632719 10 5616181 4.08E-07 4.09E-07
vg1105377726 sf1105373477 11 5377726 5.65E-07 5.65E-07
vg0712961657 sf0712960664 7 12961657 7.46E-07 7.47E-07
vg0713112667 sf0713111674 7 13112667 1.06E-06 1.06E-06
vg0728462047 sf0728461055 7 28462047 2.36E-06 2.36E-06
vg0627921096 sf0627920098 6 27921096 4.32E-06 4.32E-06