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 mr1491 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
vg1215869969 sf1215867265 12 15869969 8.86E-43 1.62E-20
vg1211103816 sf1211101182 12 11103816 8.74E-17 NA
vg0228693616 sf0228687747 2 28693616 1.40E-15 NA
vg0919147683 sf0919147272 9 19147683 5.32E-15 NA
vg0724619568 sf0724618574 7 24619568 5.97E-15 NA
vg0218132013 sf0218126144 2 18132013 8.01E-15 1.49E-06
vg1215870946 sf1215868242 12 15870946 NA 4.34E-09
vg0901048761 sf0901047761 9 1048761 NA 1.09E-07
vg1221791160 sf1221757707 12 21791160 NA 1.49E-06
vg1218663003 sf1218634438 12 18663003 NA 2.30E-06
vg1212877317 sf1212874656 12 12877317 NA 3.49E-06
vg1022588644 sf1022517118 10 22588644 NA 4.30E-06
vg0432718715 sf0432533601 4 32718715 NA 4.79E-06
vg0610620315 sf0610619316 6 10620315 NA 4.92E-06