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 mr1661 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
vg0218624032 sf0218618163 2 18624032 1.35E-09 7.42E-06
vg0219336460 sf0219330592 2 19336460 3.45E-08 4.79E-06
vg0721864182 sf0721863189 7 21864182 3.95E-08 NA
vg0128530844 sf0128529799 1 28530844 4.47E-08 NA
vg0821970212 sf0821967499 8 21970212 1.58E-06 5.55E-07
vg0317321849 sf0317320659 3 17321849 3.55E-06 5.86E-07
vg0815304114 sf0815301400 8 15304114 6.61E-06 8.30E-06
vg1214600105 sf1214597445 12 14600105 9.03E-06 NA
vg0334655144 sf0334648014 3 34655144 NA 1.84E-06
vg0526989740 sf0526927096 5 26989740 NA 2.91E-06
vg0814295706 sf0814292992 8 14295706 NA 4.34E-06
vg0421559077 sf0421387127 4 21559077 NA 5.09E-06