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Detailed information for vg1213095452:

Variant ID: vg1213095452 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 13095452
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:


ATCTAGGGCAAGCAGCAGAAGCTCTAAAATGGATCAGTAGTTGTCGAGGCAAGAAGACAACGATTTCAACCATCAGAATAAAAAAGGGCAGCCTCAAACT[C/A]
CACTCCTGACTTGGCCATGTCCAAAATCAATGTATAAAGGAAAATGGTACACATCGGCCTTCTTTTTGCGGATTGAAGATCAACAGGAGTAGCGCAACAT

Reverse complement sequence

ATGTTGCGCTACTCCTGTTGATCTTCAATCCGCAAAAAGAAGGCCGATGTGTACCATTTTCCTTTATACATTGATTTTGGACATGGCCAAGTCAGGAGTG[G/T]
AGTTTGAGGCTGCCCTTTTTTATTCTGATGGTTGAAATCGTTGTCTTCTTGCCTCGACAACTACTGATCCATTTTAGAGCTTCTGCTGCTTGCCCTAGAT

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 88.80% 0.00% 0.44% 10.75% NA
All Indica  2759 82.20% 0.00% 0.72% 17.04% NA
All Japonica  1512 97.60% 0.00% 0.07% 2.31% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.80% 0.00% 0.17% 1.01% NA
Indica II  465 60.90% 0.00% 2.15% 36.99% NA
Indica III  913 81.80% 0.10% 0.66% 17.42% NA
Indica Intermediate  786 82.70% 0.00% 0.38% 16.92% NA
Temperate Japonica  767 95.80% 0.00% 0.13% 4.04% NA
Tropical Japonica  504 99.60% 0.00% 0.00% 0.40% NA
Japonica Intermediate  241 99.20% 0.00% 0.00% 0.83% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 0.00% 0.00% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1213095452 C -> DEL LOC_Os12g23150.1 N frameshift_variant Average:66.426; most accessible tissue: Minghui63 flower, score: 81.266 N N N N
vg1213095452 C -> A LOC_Os12g23150.1 stop_gained ; p.Glu225*; HIGH stop_gained Average:66.426; most accessible tissue: Minghui63 flower, score: 81.266 N N N N