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 mr1790 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
vg0200213199 sf0200213199 2 213199 4.74E-09 8.36E-07
vg1219786034 sf1219757504 12 19786034 3.48E-08 NA
vg1218290915 sf1218262351 12 18290915 5.54E-08 NA
vg1005802057 sf1005818595 10 5802057 6.81E-08 2.43E-06
vg0200471574 sf0200471574 2 471574 1.94E-07 2.53E-06
vg0109280202 sf0109279202 1 9280202 2.44E-07 4.41E-06
vg0203000556 sf0203000554 2 3000556 2.87E-07 3.43E-06
vg1103424320 sf1103420223 11 3424320 6.93E-07 3.98E-06
vg0217181818 sf0217175948 2 17181818 8.54E-06 NA