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 mr1771 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
vg1019088726 sf1019017283 10 19088726 8.41E-53 3.26E-10
vg1019101727 sf1019030284 10 19101727 1.33E-52 1.44E-10
vg1224594467 sf1224560921 12 24594467 3.70E-48 NA
vg0106176542 sf0106175542 1 6176542 4.39E-47 NA
vg0124625557 sf0124624513 1 24625557 1.28E-46 NA
vg0132621629 sf0132620585 1 32621629 5.94E-46 NA
vg0432523918 sf0432338810 4 32523918 NA 2.11E-08
vg0826228501 sf0826225787 8 26228501 NA 2.26E-07
vg0815289622 sf0815286908 8 15289622 NA 7.15E-07
vg0235290910 sf0235285041 2 35290910 NA 8.70E-07
vg0816679648 sf0816676934 8 16679648 NA 1.76E-06
vg1006456919 sf1006472542 10 6456919 NA 2.10E-06
vg1200274541 sf1200273541 12 274541 NA 2.84E-06
vg0518984986 sf0518922470 5 18984986 NA 3.15E-06
vg0400678101 sf0400677100 4 678101 NA 3.33E-06
vg0810288130 sf0810287134 8 10288130 NA 3.71E-06
vg0133432014 sf0133430970 1 33432014 NA 3.92E-06
vg1004059501 sf1004058477 10 4059501 NA 3.98E-06
vg0820968537 sf0820965824 8 20968537 NA 4.64E-06
vg0810881067 sf0810880072 8 10881067 NA 4.71E-06