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Detailed information for vg0125056493:

Variant ID: vg0125056493 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 25056493
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: 331. )

Flanking Sequence (100 bp) in Reference Genome:


CCTCGTAAAGTATCATCGTCACCTGTATGTACCAAAGGTTAATTACCTCTAGTTGCCATGTGATTTAGTAATTTCAATATCATCTCTACATCTAAAAGAT[A/G]
ACTTAAACATGGATTTCCTAAAAAAGTTACTTAATTTCAACATTTATTACTCACGTTTTGAGTTTGCTCAGGCCTTCATAATCAAGTTTGTTTTTCTGAA

Reverse complement sequence

TTCAGAAAAACAAACTTGATTATGAAGGCCTGAGCAAACTCAAAACGTGAGTAATAAATGTTGAAATTAAGTAACTTTTTTAGGAAATCCATGTTTAAGT[T/C]
ATCTTTTAGATGTAGAGATGATATTGAAATTACTAAATCACATGGCAACTAGAGGTAATTAACCTTTGGTACATACAGGTGACGATGATACTTTACGAGG

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 99.70% 0.30% 0.00% 0.00% NA
All Indica  2759 99.60% 0.40% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 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 99.60% 0.40% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.80% 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  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0125056493 A -> G LOC_Os01g43740.1 upstream_gene_variant ; 4271.0bp to feature; MODIFIER N Average:75.302; most accessible tissue: Callus, score: 90.679 N N N N
vg0125056493 A -> G LOC_Os01g43720.1 intron_variant ; MODIFIER N Average:75.302; most accessible tissue: Callus, score: 90.679 N N N N