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 mr1043 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
vg0920389319 sf0920388838 9 20389319 2.32E-09 4.68E-06
vg0810686573 sf0810685578 8 10686573 4.91E-08 NA
vg0619155361 sf0619154364 6 19155361 5.05E-08 NA
vg0132936830 sf0132935786 1 32936830 5.34E-08 NA
vg0810647541 sf0810646545 8 10647541 3.34E-07 1.26E-06
vg0619405763 sf0619404766 6 19405763 4.71E-07 4.99E-06
vg0419763927 sf0419591962 4 19763927 3.94E-06 2.50E-06
vg0901409319 sf0901408319 9 1409319 4.53E-06 NA