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Detailed information for vg0722038252:

Variant ID: vg0722038252 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 22038252
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.02, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:


TGGTGACATGCTGCAGATCACTGTACCGGAAGGCAATCAGTGCGCCCCCTGTAGTCTTGGATATGCGAAGAGTCCTGTCTCGGCGGCATTTCTGGAATAC[G/A]
ATGAACAACACAATTGCAAGGATTATCAAAGCTGCAGCAACTCCACCTACAACTGCACCAATGATCATTTTCTTGCTCTTTTTAGAGTCTGGAAGTTCAG

Reverse complement sequence

CTGAACTTCCAGACTCTAAAAAGAGCAAGAAAATGATCATTGGTGCAGTTGTAGGTGGAGTTGCTGCAGCTTTGATAATCCTTGCAATTGTGTTGTTCAT[C/T]
GTATTCCAGAAATGCCGCCGAGACAGGACTCTTCGCATATCCAAGACTACAGGGGGCGCACTGATTGCCTTCCGGTACAGTGATCTGCAGCATGTCACCA

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 52.60% 47.40% 0.06% 0.02% NA
All Indica  2759 79.80% 20.00% 0.11% 0.04% NA
All Japonica  1512 5.90% 94.10% 0.00% 0.00% NA
Aus  269 58.00% 42.00% 0.00% 0.00% NA
Indica I  595 93.60% 6.10% 0.34% 0.00% NA
Indica II  465 76.10% 23.40% 0.22% 0.22% NA
Indica III  913 75.70% 24.30% 0.00% 0.00% NA
Indica Intermediate  786 76.50% 23.50% 0.00% 0.00% NA
Temperate Japonica  767 0.30% 99.70% 0.00% 0.00% NA
Tropical Japonica  504 13.90% 86.10% 0.00% 0.00% NA
Japonica Intermediate  241 7.10% 92.90% 0.00% 0.00% NA
VI/Aromatic  96 0.00% 100.00% 0.00% 0.00% NA
Intermediate  90 40.00% 60.00% 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
vg0722038252 G -> DEL LOC_Os07g36780.1 N frameshift_variant Average:78.71; most accessible tissue: Callus, score: 85.123 N N N N
vg0722038252 G -> A LOC_Os07g36780.1 synonymous_variant ; p.Ile461Ile; LOW synonymous_codon Average:78.71; most accessible tissue: Callus, score: 85.123 N N N N