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Detailed information for vg0526336258:

Variant ID: vg0526336258 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 26336258
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 331. )

Flanking Sequence (100 bp) in Reference Genome:


CATTTAGTACCGATCCTGTATGCTTATACTTAAATTCTGATATTAGAAAAATAATTTTTGAACTATATGCATGGCTATTCTAGAAGCATATGGACAGAAT[C/A]
TTTCTATGAGCATGCAAAAGAAGATTCCAAGCATATTAAATCAATGAGTTCCAAGCACCAAAGCCCTCTAAAATCTCACTACCTCAGCATTCAGACAAGA

Reverse complement sequence

TCTTGTCTGAATGCTGAGGTAGTGAGATTTTAGAGGGCTTTGGTGCTTGGAACTCATTGATTTAATATGCTTGGAATCTTCTTTTGCATGCTCATAGAAA[G/T]
ATTCTGTCCATATGCTTCTAGAATAGCCATGCATATAGTTCAAAAATTATTTTTCTAATATCAGAATTTAAGTATAAGCATACAGGATCGGTACTAAATG

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 99.40% 0.40% 0.21% 0.00% NA
All Indica  2759 99.00% 0.70% 0.33% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.70% 0.00% 0.34% 0.00% NA
Indica II  465 99.60% 0.00% 0.43% 0.00% NA
Indica III  913 98.00% 2.00% 0.00% 0.00% NA
Indica Intermediate  786 99.40% 0.00% 0.64% 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% 0.00% 1.11% 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
vg0526336258 C -> A LOC_Os05g45390.1 upstream_gene_variant ; 4920.0bp to feature; MODIFIER N Average:61.799; most accessible tissue: Callus, score: 86.382 N N N N
vg0526336258 C -> A LOC_Os05g45400.1 intron_variant ; MODIFIER N Average:61.799; most accessible tissue: Callus, score: 86.382 N N N N