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 mr1065 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
vg0610752378 sf0610751379 6 10752378 4.25E-09 4.25E-09
vg0139810181 sf0139809138 1 39810181 3.01E-07 3.02E-07
vg0316110441 sf0316109088 3 16110441 3.98E-07 3.99E-07
vg1203842140 sf1203841139 12 3842140 8.92E-07 8.92E-07
vg0528836055 sf0528773410 5 28836055 1.88E-06 1.88E-06
vg0233651517 sf0233645648 2 33651517 1.93E-06 1.93E-06
vg0620772509 sf0620771512 6 20772509 1.97E-06 1.97E-06
vg0419495962 sf0419324000 4 19495962 2.01E-06 2.01E-06
vg1122416969 sf1121950840 11 22416969 2.20E-06 2.20E-06
vg0506451956 sf0506451896 5 6451956 2.23E-06 2.23E-06
vg0528836237 sf0528773592 5 28836237 2.49E-06 2.50E-06
vg0703841256 sf0703840257 7 3841256 2.89E-06 2.89E-06
vg0207737895 sf0207737894 2 7737895 2.90E-06 2.90E-06
vg1125633617 sf1125167456 11 25633617 3.45E-06 3.45E-06
vg0134313386 sf0134312343 1 34313386 3.47E-06 3.47E-06
vg0626895745 sf0626894748 6 26895745 3.48E-06 3.48E-06
vg0805797889 sf0805796892 8 5797889 3.48E-06 3.48E-06
vg0320258954 sf0320257465 3 20258954 3.55E-06 3.55E-06
vg0135004297 sf0135003254 1 35004297 4.12E-06 4.12E-06
vg0419868706 sf0419696742 4 19868706 4.41E-06 4.41E-06
vg0816511732 sf0816509018 8 16511732 4.65E-06 4.65E-06