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Detailed information for vg0807859721:

Variant ID: vg0807859721 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 7859721
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGGGAGAGAAATGAGTGAAGGGGGGAGAGAATGACAAGTGGGTCCCACACCATTTTGTCACCTGGGTTGCCACGTTGGTATGCCACGTGGGCAAAAGTGG[T/C]
AAATAGTTAAGATGCCACATCTAAGAGGGGCAAAAAAAAAAGAGCAAACGTAATAAGGGTATTTGGATAATTGCCAAACCTAAAAGTGGTAAATAGTTAA

Reverse complement sequence

TTAACTATTTACCACTTTTAGGTTTGGCAATTATCCAAATACCCTTATTACGTTTGCTCTTTTTTTTTTGCCCCTCTTAGATGTGGCATCTTAACTATTT[A/G]
CCACTTTTGCCCACGTGGCATACCAACGTGGCAACCCAGGTGACAAAATGGTGTGGGACCCACTTGTCATTCTCTCCCCCCTTCACTCATTTCTCTCCCC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 73.30% 26.60% 0.08% 0.00% NA
All Indica  2759 99.10% 0.80% 0.07% 0.00% NA
All Japonica  1512 19.80% 80.10% 0.13% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.30% 0.70% 0.00% 0.00% NA
Indica II  465 97.60% 2.20% 0.22% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 99.10% 0.80% 0.13% 0.00% NA
Temperate Japonica  767 17.20% 82.70% 0.13% 0.00% NA
Tropical Japonica  504 21.00% 79.00% 0.00% 0.00% NA
Japonica Intermediate  241 25.30% 74.30% 0.41% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 75.60% 24.40% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0807859721 T -> C LOC_Os08g13219.1 upstream_gene_variant ; 1330.0bp to feature; MODIFIER silent_mutation Average:53.123; most accessible tissue: Callus, score: 75.299 N N N N
vg0807859721 T -> C LOC_Os08g13210.1 downstream_gene_variant ; 2001.0bp to feature; MODIFIER silent_mutation Average:53.123; most accessible tissue: Callus, score: 75.299 N N N N
vg0807859721 T -> C LOC_Os08g13230.1 downstream_gene_variant ; 4568.0bp to feature; MODIFIER silent_mutation Average:53.123; most accessible tissue: Callus, score: 75.299 N N N N
vg0807859721 T -> C LOC_Os08g13210-LOC_Os08g13219 intergenic_region ; MODIFIER silent_mutation Average:53.123; most accessible tissue: Callus, score: 75.299 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0807859721 1.24E-08 1.23E-08 mr1542_2 Jap_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
vg0807859721 NA 6.58E-19 mr1945_2 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
vg0807859721 9.61E-07 9.61E-07 mr1973_2 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