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 mr1354 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
vg0724482522 sf0724481528 7 24482522 1.72E-53 1.61E-44
vg0724528737 sf0724527743 7 24528737 1.77E-53 7.42E-45
vg1122418019 sf1121951890 11 22418019 1.11E-15 3.91E-09
vg1117553288 sf1117087144 11 17553288 8.92E-15 NA
vg0218382286 sf0218376417 2 18382286 5.60E-14 2.86E-08
vg0232872507 sf0232866638 2 32872507 5.70E-13 3.99E-06
vg0101018863 sf0101017863 1 1018863 3.18E-11 9.92E-07
vg0227894878 sf0227889009 2 27894878 4.57E-11 3.19E-07
vg1017000481 sf1016929253 10 17000481 5.16E-11 2.22E-06
vg0400999452 sf0400995004 4 999452 1.35E-09 3.03E-06
vg0724490397 sf0724489403 7 24490397 9.03E-09 5.09E-27
vg0103747442 sf0103746442 1 3747442 1.76E-08 2.97E-07
vg0627455814 sf0627454817 6 27455814 2.76E-06 3.95E-06
vg0319141942 sf0319140702 3 19141942 3.18E-06 3.39E-06
vg0224082355 sf0224076486 2 24082355 5.61E-06 1.87E-06
vg0724557637 sf0724556643 7 24557637 NA 2.34E-07