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 mr1480 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
vg0821991953 sf0821989240 8 21991953 6.11E-48 NA
vg0140789733 sf0140788690 1 40789733 8.18E-48 NA
vg0306755393 sf0306754393 3 6755393 2.30E-47 NA
vg0628615808 sf0628614810 6 28615808 2.45E-47 NA
vg0628822462 sf0628821464 6 28822462 5.87E-47 2.95E-07
vg0221211819 sf0221205951 2 21211819 2.36E-46 NA
vg0205305322 sf0205305321 2 5305322 8.44E-43 1.53E-08
vg0909153765 sf0909152764 9 9153765 7.16E-42 6.68E-07
vg0703673198 sf0703672199 7 3673198 NA 2.35E-07
vg0207184033 sf0207184033 2 7184033 NA 2.57E-07
vg1217925281 sf1217896715 12 17925281 NA 1.09E-06
vg0235414544 sf0235408675 2 35414544 NA 2.97E-06
vg0807974527 sf0807973531 8 7974527 NA 3.07E-06
vg0718112109 sf0718111116 7 18112109 NA 3.49E-06
vg0207220094 sf0207220094 2 7220094 NA 3.88E-06
vg0806138367 sf0806127107 8 6138367 NA 4.97E-06