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 mr1504 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
vg1107375253 sf1107370998 11 7375253 3.02E-08 2.68E-08
vg0305015386 sf0305014388 3 5015386 1.18E-07 2.74E-06
vg1116495084 sf1116029961 11 16495084 5.48E-07 9.87E-07
vg0813623119 sf0813620404 8 13623119 1.95E-06 3.02E-06
vg0814031551 sf0814028837 8 14031551 4.02E-06 NA
vg0335324797 sf0335317666 3 35324797 9.00E-06 3.50E-06