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Detailed information for vg0604193282:

Variant ID: vg0604193282 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 4193282
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: 281. )

Flanking Sequence (100 bp) in Reference Genome:


ATGTAACCTTGTTGGCGTTTGGGACTAGCTCCTGCAGCGATTTCATCCGCTCCGCTATCCTCTCCCTCCGAAGCTGAAAATAACATGAACAATACACAAA[A/G]
AGTTGAGAAGAAAAATGGAAATGTTGCTCAAGTTCCATTTATTTTTTGGTTGAAACTTGAAAGAGGCAGTAATAATTGTAAGATGATTTCGTGAACAGTG

Reverse complement sequence

CACTGTTCACGAAATCATCTTACAATTATTACTGCCTCTTTCAAGTTTCAACCAAAAAATAAATGGAACTTGAGCAACATTTCCATTTTTCTTCTCAACT[T/C]
TTTGTGTATTGTTCATGTTATTTTCAGCTTCGGAGGGAGAGGATAGCGGAGCGGATGAAATCGCTGCAGGAGCTAGTCCCAAACGCCAACAAGGTTACAT

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 99.90% 0.10% 0.00% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 98.50% 1.50% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 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
vg0604193282 A -> G LOC_Os06g08490.1 upstream_gene_variant ; 2719.0bp to feature; MODIFIER N Average:39.659; most accessible tissue: Callus, score: 67.489 N N N N
vg0604193282 A -> G LOC_Os06g08500.1 intron_variant ; MODIFIER N Average:39.659; most accessible tissue: Callus, score: 67.489 N N N N