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 mr1140 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
vg0406393570 sf0406389010 4 6393570 5.45E-144 3.35E-31
vg0406526555 sf0406521998 4 6526555 9.72E-144 9.34E-33
vg1017228554 sf1017157327 10 17228554 5.18E-109 4.29E-08
vg1017223697 sf1017152470 10 17223697 2.83E-108 7.07E-09
vg0411344776 sf0411335479 4 11344776 1.38E-106 NA
vg0305431587 sf0305430587 3 5431587 1.39E-106 NA
vg0122880113 sf0122879069 1 22880113 5.84E-105 2.06E-07
vg0614107939 sf0614106940 6 14107939 5.54E-98 4.13E-08
vg0406521772 sf0406517215 4 6521772 NA 5.00E-12
vg0619719272 sf0619718275 6 19719272 NA 2.08E-09
vg0123735612 sf0123734568 1 23735612 NA 2.03E-08
vg0412575333 sf0412566043 4 12575333 NA 7.13E-08
vg0407576542 sf0407571810 4 7576542 NA 7.19E-08
vg1122507717 sf1122041588 11 22507717 NA 8.63E-08
vg0811482287 sf0811481292 8 11482287 NA 9.57E-08
vg0406358715 sf0406354155 4 6358715 NA 9.70E-08
vg0814055215 sf0814052501 8 14055215 NA 1.34E-07
vg1209905874 sf1209903284 12 9905874 NA 1.47E-07
vg0720714007 sf0720713014 7 20714007 NA 5.19E-07
vg0233608236 sf0233602367 2 33608236 NA 5.43E-07
vg0406489536 sf0406484979 4 6489536 NA 5.81E-07
vg0619861955 sf0619860958 6 19861955 NA 6.09E-07
vg0713947405 sf0713946412 7 13947405 NA 6.35E-07
vg1100682305 sf1100681308 11 682305 NA 6.98E-07
vg0521505292 sf0521442733 5 21505292 NA 9.12E-07
vg0618064174 sf0618063177 6 18064174 NA 4.08E-06