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 mr1126 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
vg1224016863 sf1223983316 12 24016863 7.15E-11 NA
vg0827468841 sf0827466127 8 27468841 7.38E-11 NA
vg0123674628 sf0123673584 1 23674628 3.80E-10 NA
vg0434775690 sf0434590581 4 34775690 4.20E-10 NA
vg0127642064 sf0127641020 1 27642064 5.17E-10 NA
vg0500436456 sf0500436456 5 436456 2.14E-08 2.45E-06
vg1011000041 sf1010928861 10 11000041 1.46E-06 NA