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 mr1265 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
vg0710361771 sf0710360777 7 10361771 9.93E-08 4.64E-07
vg1218055139 sf1218026575 12 18055139 8.17E-07 3.31E-06
vg0128156866 sf0128155822 1 28156866 2.90E-06 4.45E-06
vg0505490581 sf0505490559 5 5490581 4.80E-06 1.71E-06
vg1209702740 sf1209700149 12 9702740 NA 8.87E-07
vg0716096216 sf0716095223 7 16096216 NA 1.16E-06
vg1017718456 sf1017647229 10 17718456 NA 1.96E-06
vg1218127273 sf1218098709 12 18127273 NA 2.44E-06
vg1116397481 sf1115932358 11 16397481 NA 8.06E-06
vg0304795782 sf0304794784 3 4795782 NA 8.64E-06