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 mr1550 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
vg0128147669 sf0128146625 1 28147669 7.48E-11 NA
vg0128139083 sf0128138039 1 28139083 2.40E-10 1.90E-06
vg0131282976 sf0131281932 1 31282976 2.18E-09 NA
vg0726946907 sf0726945913 7 26946907 1.05E-08 NA
vg0505835605 sf0505835543 5 5835605 2.19E-08 NA
vg0138616291 sf0138615248 1 38616291 3.13E-08 NA
vg0617539354 sf0617538357 6 17539354 1.86E-07 NA
vg1127763517 sf1127291903 11 27763517 1.01E-06 2.68E-06
vg0136768336 sf0136767293 1 36768336 4.81E-06 NA
vg0907175535 sf0907174535 9 7175535 NA 3.10E-06
vg0907175556 sf0907174556 9 7175556 NA 3.22E-06
vg0607988536 sf0607987537 6 7988536 NA 4.63E-06