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 mr1250 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
vg0431614108 sf0431429003 4 31614108 3.41E-08 3.41E-08
vg1005684375 sf1005700913 10 5684375 9.04E-08 9.04E-08
vg0121871143 sf0121870098 1 21871143 9.86E-08 9.86E-08
vg1009262901 sf1009191722 10 9262901 2.44E-07 2.44E-07
vg1004865986 sf1004882523 10 4865986 7.27E-07 7.27E-07
vg1009516560 sf1009445381 10 9516560 8.04E-07 8.04E-07
vg1107330232 sf1107325977 11 7330232 2.30E-06 2.30E-06
vg1022814760 sf1022743233 10 22814760 2.30E-06 2.30E-06
vg0207227884 sf0207227884 2 7227884 2.68E-06 2.68E-06
vg0431452876 sf0431267774 4 31452876 3.04E-06 3.04E-06
vg0308007821 sf0308006759 3 8007821 3.09E-06 3.09E-06
vg0324716969 sf0324715048 3 24716969 3.85E-06 3.85E-06
vg1128859381 sf1128336160 11 28859381 3.93E-06 3.93E-06