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 mr1421 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
vg0200658088 sf0200658088 2 658088 3.88E-07 3.88E-07
vg1202735550 sf1202734552 12 2735550 9.01E-07 9.03E-07
vg0122885136 sf0122884092 1 22885136 1.88E-06 1.88E-06
vg0906997533 sf0906996533 9 6997533 2.16E-06 2.16E-06
vg1215352883 sf1215350181 12 15352883 2.96E-06 2.97E-06
vg1122514350 sf1122048221 11 22514350 3.47E-06 3.47E-06
vg0103977465 sf0103976465 1 3977465 3.64E-06 3.65E-06
vg0232102665 sf0232096796 2 32102665 3.88E-06 3.89E-06
vg0307653368 sf0307652306 3 7653368 4.03E-06 4.04E-06
vg0229962990 sf0229957121 2 29962990 4.14E-06 4.15E-06
vg0522752497 sf0522689939 5 22752497 4.75E-06 4.73E-06
vg0906899491 sf0906898491 9 6899491 5.12E-06 5.13E-06