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 mr1792 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
vg0805569282 sf0805568285 8 5569282 2.81E-12 NA
vg0804751253 sf0804750256 8 4751253 4.12E-12 NA
vg0113887896 sf0113886870 1 13887896 8.38E-12 NA
vg0124234030 sf0124232986 1 24234030 3.19E-11 NA
vg1210596771 sf1210594184 12 10596771 3.21E-11 NA
vg1215558096 sf1215555393 12 15558096 9.43E-11 4.89E-08
vg0805619517 sf0805618520 8 5619517 1.75E-09 3.47E-06
vg1210023864 sf1210021275 12 10023864 9.25E-09 4.46E-07
vg0122939348 sf0122938304 1 22939348 4.54E-07 5.45E-07
vg0503485496 sf0503485473 5 3485496 8.17E-07 9.42E-06
vg0810861351 sf0810860356 8 10861351 1.63E-06 NA
vg0720903383 sf0720902390 7 20903383 NA 2.21E-06
vg1218287893 sf1218259329 12 18287893 NA 3.05E-06
vg0912640700 sf0912639699 9 12640700 NA 3.14E-06
vg0124212768 sf0124211724 1 24212768 NA 4.32E-06