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Detailed information for vg0804463753:

Variant ID: vg0804463753 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 4463753
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAAAACCGGTCGGCTTTGGCGAAATTCCGAGCGAAATCATCGAAATTTCAATCAATAACTATAAATAGAGGTAAACTAAAATTGTTTTCCTTTTTTAATT[C/A]
GTTATTCTTTTCTTTCCTATTGTAAATTTCAGTAAATACATGGAATACATCAGTTTTTTTGAAAATTTATATCCCAATAGGTTCTATGAATATCATACTA

Reverse complement sequence

TAGTATGATATTCATAGAACCTATTGGGATATAAATTTTCAAAAAAACTGATGTATTCCATGTATTTACTGAAATTTACAATAGGAAAGAAAAGAATAAC[G/T]
AATTAAAAAAGGAAAACAATTTTAGTTTACCTCTATTTATAGTTATTGATTGAAATTTCGATGATTTCGCTCGGAATTTCGCCAAAGCCGACCGGTTTTC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 36.00% 0.10% 1.27% 62.63% NA
All Indica  2759 6.20% 0.10% 1.45% 92.32% NA
All Japonica  1512 95.20% 0.10% 0.07% 4.70% NA
Aus  269 11.20% 0.00% 4.83% 84.01% NA
Indica I  595 9.60% 0.00% 1.34% 89.08% NA
Indica II  465 7.70% 0.00% 2.58% 89.68% NA
Indica III  913 2.30% 0.00% 0.77% 96.93% NA
Indica Intermediate  786 7.10% 0.30% 1.65% 90.97% NA
Temperate Japonica  767 98.30% 0.00% 0.13% 1.56% NA
Tropical Japonica  504 89.30% 0.00% 0.00% 10.71% NA
Japonica Intermediate  241 97.50% 0.40% 0.00% 2.07% NA
VI/Aromatic  96 22.90% 3.10% 3.12% 70.83% NA
Intermediate  90 43.30% 0.00% 3.33% 53.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0804463753 C -> A LOC_Os08g07900.1 upstream_gene_variant ; 3530.0bp to feature; MODIFIER silent_mutation Average:15.069; most accessible tissue: Callus, score: 29.336 N N N N
vg0804463753 C -> A LOC_Os08g07910.1 upstream_gene_variant ; 2632.0bp to feature; MODIFIER silent_mutation Average:15.069; most accessible tissue: Callus, score: 29.336 N N N N
vg0804463753 C -> A LOC_Os08g07930.1 upstream_gene_variant ; 2276.0bp to feature; MODIFIER silent_mutation Average:15.069; most accessible tissue: Callus, score: 29.336 N N N N
vg0804463753 C -> A LOC_Os08g07920.1 intron_variant ; MODIFIER silent_mutation Average:15.069; most accessible tissue: Callus, score: 29.336 N N N N
vg0804463753 C -> DEL N N silent_mutation Average:15.069; most accessible tissue: Callus, score: 29.336 N N N N