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 mr1936 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
vg0222725905 sf0222720036 2 22725905 3.77E-26 8.25E-19
vg0222719698 sf0222713829 2 22719698 3.35E-23 4.33E-16
vg0222725041 sf0222719172 2 22725041 1.31E-17 6.61E-11
vg1009142714 sf1009071575 10 9142714 1.42E-13 NA
vg1009060641 sf1008989502 10 9060641 7.97E-13 3.45E-06
vg1006498976 sf1006514599 10 6498976 2.80E-12 NA
vg1009113084 sf1009041945 10 9113084 5.61E-12 1.80E-06
vg0224284988 sf0224279119 2 24284988 2.49E-10 NA
vg0407817429 sf0407812697 4 7817429 4.25E-10 NA
vg0221953494 sf0221947625 2 21953494 2.75E-09 5.26E-07
vg0222879623 sf0222873754 2 22879623 3.55E-08 1.10E-06
vg0221968611 sf0221962742 2 21968611 2.96E-07 4.46E-06
vg1020189984 sf1020118466 10 20189984 NA 1.74E-06
vg0225037452 sf0225031583 2 25037452 NA 1.88E-06
vg0225005075 sf0224999206 2 25005075 NA 2.67E-06