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 mr1983 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
vg1016459333 sf1016388106 10 16459333 2.64E-07 2.64E-07
vg0421309810 sf0421137864 4 21309810 2.78E-07 2.78E-07
vg0420711795 sf0420539838 4 20711795 3.03E-07 3.04E-07
vg0131779655 sf0131778611 1 31779655 5.50E-07 5.51E-07
vg1016401246 sf1016330020 10 16401246 5.63E-07 5.63E-07
vg1209941601 sf1209939011 12 9941601 1.07E-06 1.07E-06
vg0826639749 sf0826637035 8 26639749 1.74E-06 1.74E-06
vg0406880594 sf0406876039 4 6880594 2.11E-06 2.11E-06
vg1122071248 sf1121605119 11 22071248 2.15E-06 2.16E-06
vg0224382110 sf0224376241 2 24382110 2.24E-06 2.24E-06
vg0717669062 sf0717668069 7 17669062 2.43E-06 2.44E-06
vg0209279511 sf0209279509 2 9279511 3.10E-06 3.10E-06
vg0715403959 sf0715402966 7 15403959 3.88E-06 3.88E-06
vg1222370405 sf1222336844 12 22370405 3.94E-06 3.94E-06
vg0816860308 sf0816857594 8 16860308 4.14E-06 4.14E-06
vg1017447725 sf1017376498 10 17447725 4.20E-06 4.20E-06
vg0421318693 sf0421146747 4 21318693 4.76E-06 4.76E-06
vg0219207534 sf0219201666 2 19207534 6.24E-06 6.24E-06