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Detailed information for vg0503844815:

Variant ID: vg0503844815 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 3844815
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTCAAAGTATAGATCGAGTTTCAATTTGATTTTTGTTGGGGTGATAGATATTTCATATTAATATACTCTACATTGTAGAAAAGCAGATTTTTTTTCACAA[C/T]
CATTTACATTAAATCTAAAGAAAGATCCCCGCAAAATTAAATCTAAAAGAAAGATGTACAGAGGGGACATCTCTGGATTAGAATCCATTCCGTGGAATTA

Reverse complement sequence

TAATTCCACGGAATGGATTCTAATCCAGAGATGTCCCCTCTGTACATCTTTCTTTTAGATTTAATTTTGCGGGGATCTTTCTTTAGATTTAATGTAAATG[G/A]
TTGTGAAAAAAAATCTGCTTTTCTACAATGTAGAGTATATTAATATGAAATATCTATCACCCCAACAAAAATCAAATTGAAACTCGATCTATACTTTGAG

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 99.30% 0.60% 0.13% 0.00% NA
All Indica  2759 100.00% 0.00% 0.04% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 88.10% 10.00% 1.86% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.00% 0.11% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0503844815 C -> T LOC_Os05g07260.1 downstream_gene_variant ; 1646.0bp to feature; MODIFIER silent_mutation Average:32.356; most accessible tissue: Callus, score: 65.885 N N N N
vg0503844815 C -> T LOC_Os05g07260.2 downstream_gene_variant ; 1657.0bp to feature; MODIFIER silent_mutation Average:32.356; most accessible tissue: Callus, score: 65.885 N N N N
vg0503844815 C -> T LOC_Os05g07260.4 downstream_gene_variant ; 1657.0bp to feature; MODIFIER silent_mutation Average:32.356; most accessible tissue: Callus, score: 65.885 N N N N
vg0503844815 C -> T LOC_Os05g07260.3 downstream_gene_variant ; 1646.0bp to feature; MODIFIER silent_mutation Average:32.356; most accessible tissue: Callus, score: 65.885 N N N N
vg0503844815 C -> T LOC_Os05g07270.1 intron_variant ; MODIFIER silent_mutation Average:32.356; most accessible tissue: Callus, score: 65.885 N N N N