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 mr1200 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
vg0610582344 sf0610581345 6 10582344 9.36E-42 1.23E-25
vg0610566237 sf0610565238 6 10566237 1.05E-41 1.35E-29
vg0610872773 sf0610871774 6 10872773 2.89E-21 1.19E-12
vg0610626135 sf0610625136 6 10626135 1.09E-15 1.60E-09
vg0610444061 sf0610443062 6 10444061 3.48E-15 6.13E-15
vg0611098730 sf0611097731 6 11098730 4.48E-15 2.52E-11
vg0610573005 sf0610572006 6 10573005 8.96E-15 7.22E-11
vg0610965158 sf0610964159 6 10965158 1.63E-13 4.83E-10
vg0610435285 sf0610434286 6 10435285 3.45E-13 3.91E-13
vg0610379141 sf0610378142 6 10379141 1.93E-11 6.29E-07
vg0611426472 sf0611425473 6 11426472 8.16E-11 2.06E-06
vg0610119624 sf0610118625 6 10119624 3.79E-10 2.62E-13
vg0617815455 sf0617814458 6 17815455 7.63E-10 5.92E-07
vg0610390138 sf0610389139 6 10390138 6.93E-09 4.19E-08
vg0610750291 sf0610749292 6 10750291 1.03E-08 8.73E-08
vg0611392640 sf0611391641 6 11392640 1.63E-08 3.80E-07
vg0610903539 sf0610902540 6 10903539 1.52E-07 1.95E-08
vg0615048731 sf0615047732 6 15048731 NA 5.94E-09
vg0613809145 sf0613808146 6 13809145 NA 2.16E-08
vg0618988041 sf0618987044 6 18988041 NA 2.46E-07
vg0617926432 sf0617925435 6 17926432 NA 3.41E-07
vg0611588314 sf0611587315 6 11588314 NA 9.73E-07