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 mr1780 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
vg1215969828 sf1215967124 12 15969828 1.06E-42 1.72E-08
vg1215973361 sf1215970657 12 15973361 1.24E-42 8.38E-09
vg1209209302 sf1209206711 12 9209302 1.83E-40 2.41E-06
vg0216253712 sf0216247842 2 16253712 5.30E-39 NA
vg0805964617 sf0805963620 8 5964617 1.03E-37 NA
vg0719010690 sf0719009697 7 19010690 8.20E-37 NA
vg0614107939 sf0614106940 6 14107939 4.95E-36 4.55E-06
vg0617331761 sf0617330764 6 17331761 3.81E-35 3.71E-06
vg1023134936 sf1023063408 10 23134936 NA 6.22E-07
vg1121965345 sf1121499216 11 21965345 NA 1.64E-06
vg1122643280 sf1122177151 11 22643280 NA 4.39E-06
vg1003175110 sf1003174087 10 3175110 NA 4.89E-06