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 mr1829 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
vg0724516475 sf0724515481 7 24516475 1.52E-35 2.85E-27
vg0724490482 sf0724489488 7 24490482 5.56E-35 1.59E-27
vg0526267993 sf0526205357 5 26267993 8.68E-13 NA
vg0724515873 sf0724514879 7 24515873 1.92E-12 5.23E-08
vg0400999452 sf0400995004 4 999452 1.19E-11 7.44E-07
vg1117553288 sf1117087144 11 17553288 2.31E-11 NA
vg0108352749 sf0108351749 1 8352749 2.46E-11 NA
vg0724745375 sf0724744381 7 24745375 6.87E-10 1.03E-06
vg1210687991 sf1210685404 12 10687991 8.97E-10 3.63E-06
vg0622686065 sf0622685068 6 22686065 9.50E-09 1.56E-06
vg0724490397 sf0724489403 7 24490397 5.73E-08 6.08E-16
vg0808091194 sf0808090198 8 8091194 9.48E-08 7.56E-07
vg0401023830 sf0401019382 4 1023830 1.51E-06 5.00E-07
vg0432639639 sf0432454528 4 32639639 7.53E-06 3.40E-06
vg0712740849 sf0712739856 7 12740849 8.60E-06 1.23E-06
vg0824471012 sf0824468298 8 24471012 NA 3.28E-06