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Detailed information for vg1213095434:

Variant ID: vg1213095434 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 13095434
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:


CTTTTGGACAATAAGTTGATCTAGGGCAAGCAGCAGAAGCTCTAAAATGGATCAGTAGTTGTCGAGGCAAGAAGACAACGATTTCAACCATCAGAATAAA[A/G]
AAGGGCAGCCTCAAACTCCACTCCTGACTTGGCCATGTCCAAAATCAATGTATAAAGGAAAATGGTACACATCGGCCTTCTTTTTGCGGATTGAAGATCA

Reverse complement sequence

TGATCTTCAATCCGCAAAAAGAAGGCCGATGTGTACCATTTTCCTTTATACATTGATTTTGGACATGGCCAAGTCAGGAGTGGAGTTTGAGGCTGCCCTT[T/C]
TTTATTCTGATGGTTGAAATCGTTGTCTTCTTGCCTCGACAACTACTGATCCATTTTAGAGCTTCTGCTGCTTGCCCTAGATCAACTTATTGTCCAAAAG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 88.80% 0.00% 0.47% 10.75% NA
All Indica  2759 82.20% 0.00% 0.76% 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 82.60% 0.00% 0.51% 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
vg1213095434 A -> DEL LOC_Os12g23150.1 N frameshift_variant Average:65.526; most accessible tissue: Zhenshan97 young leaf, score: 80.589 N N N N
vg1213095434 A -> G LOC_Os12g23150.1 missense_variant ; p.Phe231Leu; MODERATE nonsynonymous_codon ; F231L Average:65.526; most accessible tissue: Zhenshan97 young leaf, score: 80.589 unknown unknown DELETERIOUS 0.00