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 mr1754 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
vg0331365360 sf0331358245 3 31365360 4.83E-25 NA
vg0623708734 sf0623707737 6 23708734 2.20E-23 NA
vg0420665008 sf0420493051 4 20665008 3.20E-23 NA
vg0221053349 sf0221047481 2 21053349 6.58E-23 NA
vg1014199230 sf1014127996 10 14199230 6.92E-23 NA
vg0813540176 sf0813537729 8 13540176 NA 9.45E-08
vg0520099677 sf0520037152 5 20099677 NA 7.18E-07
vg1208638516 sf1208635923 12 8638516 NA 1.07E-06
vg0716748284 sf0716747291 7 16748284 NA 1.41E-06
vg0517141494 sf0517081135 5 17141494 NA 2.10E-06
vg0320737151 sf0320735661 3 20737151 NA 2.86E-06
vg0517141441 sf0517081082 5 17141441 NA 3.34E-06
vg0717472303 sf0717471310 7 17472303 NA 3.50E-06
vg0613699047 sf0613698048 6 13699047 NA 4.13E-06
vg0517141450 sf0517081091 5 17141450 NA 4.87E-06
vg0309093045 sf0309091981 3 9093045 NA 4.91E-06
vg0714392517 sf0714391524 7 14392517 NA 4.99E-06
vg0911407067 sf0911406066 9 11407067 NA 6.84E-06
vg0415467485 sf0415458170 4 15467485 NA 7.02E-06
vg0412476851 sf0412467566 4 12476851 NA 7.83E-06