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Detailed information for vg0420970814:

Variant ID: vg0420970814 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 20970814
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


AACAAGTTTTTCTTGTATGACATCCACCTATCTACGATTTATGTTGCCCTTCTCTTCAACTATGAGCCTTATCTTTATGCCTTACCATTTTGTCATTATA[A/G]
TACCTTGTTAATTCGCTCAGCAAAGAAATCATACATGGGCATGGCACTTTTAAATTTATTTTGCTGGAGTACACAGAGATCTTTCACTAGCTTAGATTTG

Reverse complement sequence

CAAATCTAAGCTAGTGAAAGATCTCTGTGTACTCCAGCAAAATAAATTTAAAAGTGCCATGCCCATGTATGATTTCTTTGCTGAGCGAATTAACAAGGTA[T/C]
TATAATGACAAAATGGTAAGGCATAAAGATAAGGCTCATAGTTGAAGAGAAGGGCAACATAAATCGTAGATAGGTGGATGTCATACAAGAAAAACTTGTT

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 69.10% 0.20% 1.27% 29.37% NA
All Indica  2759 47.80% 0.40% 2.14% 49.69% NA
All Japonica  1512 99.80% 0.00% 0.00% 0.20% NA
Aus  269 99.30% 0.00% 0.00% 0.74% NA
Indica I  595 78.50% 0.00% 0.67% 20.84% NA
Indica II  465 22.60% 0.00% 1.51% 75.91% NA
Indica III  913 45.80% 1.10% 3.18% 49.95% NA
Indica Intermediate  786 41.90% 0.00% 2.42% 55.73% NA
Temperate Japonica  767 99.90% 0.00% 0.00% 0.13% NA
Tropical Japonica  504 99.60% 0.00% 0.00% 0.40% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 0.00% 1.04% 0.00% NA
Intermediate  90 85.60% 1.10% 0.00% 13.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0420970814 A -> DEL N N silent_mutation Average:10.675; most accessible tissue: Zhenshan97 panicle, score: 24.575 N N N N
vg0420970814 A -> G LOC_Os04g34670.1 intron_variant ; MODIFIER silent_mutation Average:10.675; most accessible tissue: Zhenshan97 panicle, score: 24.575 N N N N