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 mr1062 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
vg0405559327 sf0405554768 4 5559327 3.97E-30 5.12E-14
vg0405599476 sf0405594917 4 5599476 2.40E-29 1.09E-15
vg0410985561 sf0410976262 4 10985561 3.52E-23 1.32E-08
vg0405735471 sf0405730910 4 5735471 6.73E-23 6.34E-15
vg0405737766 sf0405733205 4 5737766 9.49E-23 2.46E-15
vg0806183176 sf0806182181 8 6183176 2.69E-22 1.91E-07
vg0302819004 sf0302818000 3 2819004 2.51E-21 7.38E-06
vg0806333851 sf0806332856 8 6333851 3.64E-21 2.91E-09
vg0405540593 sf0405536034 4 5540593 1.06E-19 4.29E-15
vg0412793995 sf0412784705 4 12793995 3.89E-18 3.07E-07
vg0405442580 sf0405438021 4 5442580 9.45E-18 3.15E-08
vg0405856827 sf0405852268 4 5856827 2.62E-15 2.91E-07
vg0103126664 sf0103125664 1 3126664 1.59E-14 NA
vg0405563927 sf0405559368 4 5563927 NA 2.90E-14
vg0405244056 sf0405239497 4 5244056 NA 1.40E-10
vg0408634359 sf0408629633 4 8634359 NA 1.09E-09
vg0218297603 sf0218291734 2 18297603 NA 1.78E-09
vg0405089971 sf0405085412 4 5089971 NA 1.09E-08
vg0405152405 sf0405147847 4 5152405 NA 3.10E-08
vg0803241999 sf0803241002 8 3241999 NA 3.22E-08
vg0803262566 sf0803261569 8 3262566 NA 7.89E-08
vg0627991714 sf0627990716 6 27991714 NA 9.22E-08
vg0219346384 sf0219340516 2 19346384 NA 1.10E-07
vg1002594715 sf1002593692 10 2594715 NA 1.55E-07
vg0405437883 sf0405433324 4 5437883 NA 1.93E-07
vg1006264139 sf1006279762 10 6264139 NA 2.65E-07
vg1004708904 sf1004725441 10 4708904 NA 3.86E-07
vg0124773317 sf0124772273 1 24773317 NA 4.79E-07
vg0627972942 sf0627971944 6 27972942 NA 6.90E-07