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 mr1386 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
vg0229949816 sf0229943947 2 29949816 1.80E-28 5.14E-06
vg0324612598 sf0324610677 3 24612598 5.43E-28 1.80E-06
vg0324613201 sf0324611280 3 24613201 2.11E-27 NA
vg0233688245 sf0233682376 2 33688245 2.49E-27 NA
vg0914796762 sf0914795761 9 14796762 8.07E-27 NA
vg1202258122 sf1202257122 12 2258122 1.33E-26 NA
vg0234359233 sf0234353364 2 34359233 2.51E-26 3.99E-06
vg0509823730 sf0509823659 5 9823730 NA 2.26E-07
vg0909782889 sf0909781888 9 9782889 NA 2.33E-07
vg0808580570 sf0808579574 8 8580570 NA 5.26E-07
vg0909780560 sf0909779559 9 9780560 NA 5.32E-07
vg0509682776 sf0509682705 5 9682776 NA 5.90E-07
vg0206487586 sf0206487586 2 6487586 NA 1.12E-06
vg0709235717 sf0709234723 7 9235717 NA 1.69E-06
vg0610886119 sf0610885120 6 10886119 NA 2.32E-06
vg0318084743 sf0318083525 3 18084743 NA 3.63E-06
vg0800508250 sf0800507250 8 508250 NA 7.84E-06