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 mr1868 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
vg0222724011 sf0222718142 2 22724011 1.50E-43 5.32E-35
vg0222725103 sf0222719234 2 22725103 1.64E-43 2.53E-35
vg0222765370 sf0222759501 2 22765370 1.36E-12 3.57E-07
vg0222864947 sf0222859078 2 22864947 2.67E-11 2.74E-10
vg0222879623 sf0222873754 2 22879623 3.30E-11 1.73E-11
vg0224013851 sf0224007982 2 24013851 1.44E-10 2.16E-08
vg0222730936 sf0222725067 2 22730936 3.47E-10 4.32E-06
vg0222634177 sf0222628308 2 22634177 9.10E-10 4.13E-06
vg0223720087 sf0223714218 2 23720087 2.06E-09 1.35E-08
vg0222672641 sf0222666772 2 22672641 6.33E-09 3.49E-08
vg0222799001 sf0222793132 2 22799001 9.52E-09 8.10E-08
vg0224056673 sf0224050804 2 24056673 2.24E-08 5.22E-07
vg0224872829 sf0224866960 2 24872829 2.44E-08 5.86E-07
vg0224832469 sf0224826600 2 24832469 3.48E-08 5.03E-08
vg0610463015 sf0610462016 6 10463015 1.80E-06 1.78E-06
vg0225037147 sf0225031278 2 25037147 3.13E-06 2.99E-06
vg0223039697 sf0223033828 2 23039697 6.97E-06 3.43E-07
vg0321774470 sf0321772980 3 21774470 9.55E-06 NA
vg0525239875 sf0525177296 5 25239875 NA 2.19E-06
vg0222546189 sf0222540320 2 22546189 NA 2.75E-06
vg1012841072 sf1012769887 10 12841072 NA 3.02E-06
vg1212631142 sf1212628481 12 12631142 NA 3.69E-06