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Detailed information for vg0708358657:

Variant ID: vg0708358657 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 8358657
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCGTTGGCTGATGATCGATGATCTCCGTCGCCTAGCAGTTCTTCTCCGGCTTGGTGAGCTTGCACTTGACCTTCTGGAACGCCACGGAGGTGGTGCCCGG[C/T]
GGCGCGAGCTGCAGCTTGAGCGGGCACGTCGCCTCGATCTTGCACTTGGTGAGCCTCGCCGTGTACCTCACCTCGCCGGCGATCGCCACCTCCACCTCGA

Reverse complement sequence

TCGAGGTGGAGGTGGCGATCGCCGGCGAGGTGAGGTACACGGCGAGGCTCACCAAGTGCAAGATCGAGGCGACGTGCCCGCTCAAGCTGCAGCTCGCGCC[G/A]
CCGGGCACCACCTCCGTGGCGTTCCAGAAGGTCAAGTGCAAGCTCACCAAGCCGGAGAAGAACTGCTAGGCGACGGAGATCATCGATCATCAGCCAACGA

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 95.70% 4.30% 0.00% 0.00% NA
All Indica  2759 96.30% 3.70% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 64.30% 35.70% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 93.90% 6.10% 0.00% 0.00% NA
Indica Intermediate  786 94.10% 5.90% 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 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg0708358657 C -> T LOC_Os07g14660.1 synonymous_variant ; p.Pro183Pro; LOW synonymous_codon Average:65.39; most accessible tissue: Zhenshan97 young leaf, score: 81.6 N N N N