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Detailed information for vg0804462517:

Variant ID: vg0804462517 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 4462517
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTGTAATAAGCCATCAGCAGGAGAGAGGCGAGGGCCTCATCAAGGGGATCATTCGCAAGCTGAAGAAGCTGAGAGCTCGCCATGAGATTGCCAACCAGAT[C/T]
GAGGCACTCAAGGCCCATGTCGTCGAGGAGAGCAAGCGACACAAGAGGTATGATCTTCTCAAGCCATGGTCCAGCAGCTCTGCCACTTTTACTATCGACC

Reverse complement sequence

GGTCGATAGTAAAAGTGGCAGAGCTGCTGGACCATGGCTTGAGAAGATCATACCTCTTGTGTCGCTTGCTCTCCTCGACGACATGGGCCTTGAGTGCCTC[G/A]
ATCTGGTTGGCAATCTCATGGCGAGCTCTCAGCTTCTTCAGCTTGCGAATGATCCCCTTGATGAGGCCCTCGCCTCTCTCCTGCTGATGGCTTATTACAC

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 33.90% 0.90% 1.67% 63.52% NA
All Indica  2759 5.80% 0.00% 1.16% 93.04% NA
All Japonica  1512 91.20% 2.90% 1.12% 4.76% NA
Aus  269 3.70% 0.00% 7.06% 89.22% NA
Indica I  595 8.10% 0.00% 1.51% 90.42% NA
Indica II  465 8.40% 0.00% 1.08% 90.54% NA
Indica III  913 2.70% 0.00% 0.55% 96.71% NA
Indica Intermediate  786 6.10% 0.00% 1.65% 92.24% NA
Temperate Japonica  767 91.80% 5.00% 1.69% 1.56% NA
Tropical Japonica  504 88.30% 0.40% 0.60% 10.71% NA
Japonica Intermediate  241 95.40% 1.70% 0.41% 2.49% NA
VI/Aromatic  96 14.60% 0.00% 8.33% 77.08% NA
Intermediate  90 42.20% 0.00% 3.33% 54.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0804462517 C -> T LOC_Os08g07920.1 synonymous_variant ; p.Ile123Ile; LOW synonymous_codon Average:12.914; most accessible tissue: Callus, score: 76.262 N N N N
vg0804462517 C -> DEL LOC_Os08g07920.1 N frameshift_variant Average:12.914; most accessible tissue: Callus, score: 76.262 N N N N