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 mr1097 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
vg0623248264 sf0623247267 6 23248264 4.70E-17 2.65E-06
vg0135794714 sf0135793671 1 35794714 2.18E-16 2.00E-06
vg0133154189 sf0133153145 1 33154189 4.49E-15 1.95E-06
vg1115409967 sf1114946279 11 15409967 5.19E-15 6.68E-06
vg1203607472 sf1203606471 12 3607472 2.09E-14 NA
vg1115489572 sf1115025885 11 15489572 2.80E-13 3.75E-07
vg0130732040 sf0130730996 1 30732040 1.12E-09 5.60E-17
vg0130500745 sf0130499701 1 30500745 NA 1.04E-07
vg0134539333 sf0134538290 1 34539333 NA 1.81E-07
vg0708063657 sf0708062662 7 8063657 NA 1.33E-06
vg0130922613 sf0130921569 1 30922613 NA 1.79E-06
vg0311538058 sf0311536776 3 11538058 NA 3.58E-06
vg0135645855 sf0135644812 1 35645855 NA 3.77E-06
vg0907140771 sf0907139771 9 7140771 NA 4.59E-06