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Detailed information for vg0717634270:

Variant ID: vg0717634270 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 17634270
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTTCAAGGCCCGGTGATTTTGTCCCGGCCCAGGCATAGCACGGCTCGACTCTGGTCGTGCCTATGTCGGCCCAGCCCAACAGCCATGCTGTGTCTGGGCT[A/G]
CTACTTCGGTACGCTAGGCTGGCAAGGCCAGGCCCAAAGTTTAGGGATACGAAACAGATTTATTCTCAACCATATTTAAGGCACGTCAAAAAAATAGGGA

Reverse complement sequence

TCCCTATTTTTTTGACGTGCCTTAAATATGGTTGAGAATAAATCTGTTTCGTATCCCTAAACTTTGGGCCTGGCCTTGCCAGCCTAGCGTACCGAAGTAG[T/C]
AGCCCAGACACAGCATGGCTGTTGGGCTGGGCCGACATAGGCACGACCAGAGTCGAGCCGTGCTATGCCTGGGCCGGGACAAAATCACCGGGCCTTGAAC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 42.60% 16.30% 3.41% 37.69% NA
All Indica  2759 40.20% 1.60% 2.83% 55.31% NA
All Japonica  1512 49.90% 35.30% 4.56% 10.19% NA
Aus  269 6.30% 63.90% 4.09% 25.65% NA
Indica I  595 48.90% 0.50% 5.21% 45.38% NA
Indica II  465 19.60% 1.30% 2.15% 76.99% NA
Indica III  913 42.20% 0.50% 1.53% 55.75% NA
Indica Intermediate  786 43.60% 3.90% 2.93% 49.49% NA
Temperate Japonica  767 55.10% 38.10% 5.87% 0.91% NA
Tropical Japonica  504 38.10% 36.90% 2.78% 22.22% NA
Japonica Intermediate  241 58.10% 23.20% 4.15% 14.52% NA
VI/Aromatic  96 91.70% 2.10% 0.00% 6.25% NA
Intermediate  90 50.00% 17.80% 3.33% 28.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0717634270 A -> DEL N N silent_mutation Average:15.519; most accessible tissue: Callus, score: 99.071 N N N N
vg0717634270 A -> G LOC_Os07g29950.1 upstream_gene_variant ; 892.0bp to feature; MODIFIER silent_mutation Average:15.519; most accessible tissue: Callus, score: 99.071 N N N N
vg0717634270 A -> G LOC_Os07g29940-LOC_Os07g29950 intergenic_region ; MODIFIER silent_mutation Average:15.519; most accessible tissue: Callus, score: 99.071 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0717634270 NA 2.71E-07 mr1053 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
vg0717634270 NA 1.83E-07 mr1058 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
vg0717634270 NA 7.15E-08 mr1345 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
vg0717634270 NA 3.50E-08 mr1358 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
vg0717634270 NA 3.60E-06 mr1358 Jap_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
vg0717634270 NA 6.93E-08 mr1427 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
vg0717634270 NA 3.07E-06 mr1432 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
vg0717634270 NA 7.08E-09 mr1559 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
vg0717634270 NA 6.35E-08 mr1614 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
vg0717634270 NA 3.52E-06 mr1634 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
vg0717634270 NA 3.33E-07 mr1763 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