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Detailed information for vg0708358798:

Variant ID: vg0708358798 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 8358798
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGCACTTGGTGAGCCTCGCCGTGTACCTCACCTCGCCGGCGATCGCCACCTCCACCTCGAACGTCCCCTTGGCGCTCTCCTTCCTGTACTCCTGGGCGCC[G/A]
GCGTTGCCCAGCGCCGGGACGATCGCGCCCTCGCTGCCGGACGACAGCCGGTGCACCACCGTCTTGCCGGGGCCGAGCTTGTCGCCCTTGTCGGCGAGCT

Reverse complement sequence

AGCTCGCCGACAAGGGCGACAAGCTCGGCCCCGGCAAGACGGTGGTGCACCGGCTGTCGTCCGGCAGCGAGGGCGCGATCGTCCCGGCGCTGGGCAACGC[C/T]
GGCGCCCAGGAGTACAGGAAGGAGAGCGCCAAGGGGACGTTCGAGGTGGAGGTGGCGATCGCCGGCGAGGTGAGGTACACGGCGAGGCTCACCAAGTGCA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.50% 2.50% 0.00% 0.00% NA
All Indica  2759 96.70% 3.30% 0.00% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.50% 0.50% 0.00% 0.00% NA
Indica II  465 98.30% 1.70% 0.00% 0.00% NA
Indica III  913 99.20% 0.80% 0.00% 0.00% NA
Indica Intermediate  786 90.70% 9.30% 0.00% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 78.10% 21.90% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0708358798 G -> A LOC_Os07g14660.1 synonymous_variant ; p.Ala136Ala; LOW synonymous_codon Average:74.962; most accessible tissue: Zhenshan97 young leaf, score: 82.077 N N N N