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 mr1040 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
vg0810647541 sf0810646545 8 10647541 1.69E-08 8.65E-08
vg1208226380 sf1208223785 12 8226380 3.93E-08 5.95E-07
vg0817655895 sf0817653182 8 17655895 2.56E-07 9.21E-08
vg1003557200 sf1003556177 10 3557200 3.14E-06 1.29E-06
vg0816276034 sf0816273320 8 16276034 5.37E-06 1.22E-06
vg0432860646 sf0432675533 4 32860646 6.87E-06 1.80E-07
vg0914463142 sf0914462141 9 14463142 8.54E-06 2.96E-06
vg1000804159 sf1000803135 10 804159 NA 2.69E-07
vg1213526586 sf1213523924 12 13526586 NA 7.48E-07
vg1214785844 sf1214783185 12 14785844 NA 1.31E-06
vg0129442068 sf0129441023 1 29442068 NA 3.13E-06
vg0413426647 sf0413417361 4 13426647 NA 3.70E-06