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 mr1329 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
vg1115971998 sf1115506870 11 15971998 3.58E-07 3.58E-07
vg0312663464 sf0312662182 3 12663464 9.93E-07 9.93E-07
vg0330512638 sf0330505527 3 30512638 1.68E-06 1.68E-06
vg0805869798 sf0805868801 8 5869798 1.78E-06 1.78E-06
vg1216930858 sf1216924812 12 16930858 2.40E-06 2.40E-06
vg1121167517 sf1120701396 11 21167517 2.66E-06 2.66E-06
vg0904778371 sf0904777371 9 4778371 2.67E-06 2.67E-06
vg1216589226 sf1216586519 12 16589226 2.76E-06 2.76E-06
vg1215769535 sf1215766832 12 15769535 3.03E-06 3.03E-06
vg0122336837 sf0122335792 1 22336837 3.23E-06 3.23E-06
vg1117548109 sf1117081965 11 17548109 3.97E-06 3.98E-06
vg0622510881 sf0622509884 6 22510881 4.87E-06 4.88E-06