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Detailed information for vg0725375367:

Variant ID: vg0725375367 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 25375367
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 300. )

Flanking Sequence (100 bp) in Reference Genome:


TTATGTGATCAATTTATCATGCAGGTGACTTGAATCTAAACATTATTCCTTCTGCACGGTGCCTGCTCCACGATACTGGCGTTGAAGCAGTGAGAACAGG[C/T]
CATGCGGAGCTCCCCCGAATAAAAGTTTCCAACTTGTAAATTATGCAGCTGTAGGAAATCCCAGCTATTGAGGCGCCCATCCTACTTAGGCTCTTAGACT

Reverse complement sequence

AGTCTAAGAGCCTAAGTAGGATGGGCGCCTCAATAGCTGGGATTTCCTACAGCTGCATAATTTACAAGTTGGAAACTTTTATTCGGGGGAGCTCCGCATG[G/A]
CCTGTTCTCACTGCTTCAACGCCAGTATCGTGGAGCAGGCACCGTGCAGAAGGAATAATGTTTAGATTCAAGTCACCTGCATGATAAATTGATCACATAA

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 99.80% 0.10% 0.11% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 99.30% 0.40% 0.33% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 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  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 99.50% 0.00% 0.52% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 97.10% 2.50% 0.41% 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
vg0725375367 C -> T LOC_Os07g42400.1 synonymous_variant ; p.Gly730Gly; LOW N Average:67.176; most accessible tissue: Zhenshan97 flower, score: 83.061 N N N N
vg0725375367 C -> T LOC_Os07g42400.2 3_prime_UTR_variant ; 404.0bp to feature; MODIFIER N Average:67.176; most accessible tissue: Zhenshan97 flower, score: 83.061 N N N N
vg0725375367 C -> T LOC_Os07g42395.1 upstream_gene_variant ; 3560.0bp to feature; MODIFIER N Average:67.176; most accessible tissue: Zhenshan97 flower, score: 83.061 N N N N
vg0725375367 C -> T LOC_Os07g42395.2 upstream_gene_variant ; 3511.0bp to feature; MODIFIER N Average:67.176; most accessible tissue: Zhenshan97 flower, score: 83.061 N N N N