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 mr1760 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
vg1219246262 sf1219217732 12 19246262 4.51E-07 4.53E-07
vg0131768329 sf0131767285 1 31768329 5.23E-07 5.25E-07
vg0131782565 sf0131781521 1 31782565 5.56E-07 5.57E-07
vg0417993690 sf0417821731 4 17993690 6.62E-07 6.63E-07
vg0904629329 sf0904628329 9 4629329 1.21E-06 1.22E-06
vg0606329912 sf0606328913 6 6329912 1.52E-06 1.53E-06
vg1121939108 sf1121472979 11 21939108 1.64E-06 1.65E-06
vg0801697883 sf0801696886 8 1697883 1.96E-06 1.97E-06
vg0515367140 sf0515309681 5 15367140 2.24E-06 2.25E-06
vg1213372469 sf1213369807 12 13372469 3.17E-06 3.19E-06
vg1115141419 sf1114677733 11 15141419 3.62E-06 3.64E-06
vg0528836237 sf0528773592 5 28836237 3.83E-06 3.84E-06
vg0420583670 sf0420411714 4 20583670 4.21E-06 4.23E-06
vg1011521268 sf1011450087 10 11521268 4.79E-06 4.78E-06
vg0141860740 sf0141859697 1 41860740 4.95E-06 4.98E-06
vg0806058149 sf0806057154 8 6058149 7.08E-06 7.10E-06