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Detailed information for vg0619886817:

Variant ID: vg0619886817 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 19886817
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGCCACAACAACCTCAAGGGACACCTCAACAGCGGCCATGGGCCGATTTGATTGCAGATGTCATGAAGGAGCAGTTCGGGCTCAGGCCGAAAGATGTTGG[G/A]
AATCTATATCGATAGCCATATCCTGAATTGTTTGAGAGAGTTCCTTTACCTAACCGGTTCAAAGTTCCAAATTTTTCAAAGTTCTCAGGGCAAGATAGTA

Reverse complement sequence

TACTATCTTGCCCTGAGAACTTTGAAAAATTTGGAACTTTGAACCGGTTAGGTAAAGGAACTCTCTCAAACAATTCAGGATATGGCTATCGATATAGATT[C/T]
CCAACATCTTTCGGCCTGAGCCCGAACTGCTCCTTCATGACATCTGCAATCAAATCGGCCCATGGCCGCTGTTGAGGTGTCCCTTGAGGTTGTTGTGGCA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 34.00% 0.20% 1.82% 64.01% NA
All Indica  2759 4.10% 0.30% 1.09% 94.56% NA
All Japonica  1512 95.90% 0.00% 0.13% 3.97% NA
Aus  269 0.00% 0.00% 0.00% 100.00% NA
Indica I  595 2.70% 0.50% 1.01% 95.80% NA
Indica II  465 5.20% 0.20% 0.43% 94.19% NA
Indica III  913 2.00% 0.30% 1.53% 96.17% NA
Indica Intermediate  786 6.90% 0.10% 1.02% 91.98% NA
Temperate Japonica  767 97.10% 0.00% 0.00% 2.87% NA
Tropical Japonica  504 93.50% 0.00% 0.00% 6.55% NA
Japonica Intermediate  241 97.10% 0.00% 0.83% 2.07% NA
VI/Aromatic  96 1.00% 0.00% 51.04% 47.92% NA
Intermediate  90 48.90% 0.00% 5.56% 45.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0619886817 G -> A LOC_Os06g34140.1 intron_variant ; MODIFIER silent_mutation Average:14.436; most accessible tissue: Callus, score: 33.431 N N N N
vg0619886817 G -> DEL N N silent_mutation Average:14.436; most accessible tissue: Callus, score: 33.431 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0619886817 NA 1.47E-07 mr1145 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0619886817 NA 2.86E-08 mr1241 Ind_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0619886817 NA 3.08E-08 mr1301 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0619886817 NA 3.77E-07 mr1411 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0619886817 NA 8.82E-06 mr1436 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0619886817 NA 6.52E-06 mr1437 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0619886817 NA 4.32E-09 mr1722 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0619886817 NA 6.29E-06 mr1805 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0619886817 NA 3.61E-08 mr1973 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0619886817 NA 9.32E-07 mr1970_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0619886817 NA 1.30E-07 mr1973_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251