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Detailed information for vg1101255723:

Variant ID: vg1101255723 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 1255723
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:


GATTACGGTACGCATCTATCTTCCTATGAAATGTTCTCTCTTGTTTTCAATAAAACTATGCTTGCACTGAATCATTTGTTTTTATAATTTTGCAGGACAA[G/A]
TTTGAAAATGAAGATCCAGATATTAAAATTGATGTATACAAAGATGAGATAATGGAACATGCCAAGTCTCTTTGGATTAACTGGCGTGGAGATTTGCATC

Reverse complement sequence

GATGCAAATCTCCACGCCAGTTAATCCAAAGAGACTTGGCATGTTCCATTATCTCATCTTTGTATACATCAATTTTAATATCTGGATCTTCATTTTCAAA[C/T]
TTGTCCTGCAAAATTATAAAAACAAATGATTCAGTGCAAGCATAGTTTTATTGAAAACAAGAGAGAACATTTCATAGGAAGATAGATGCGTACCGTAATC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 64.50% 4.30% 1.78% 29.45% NA
All Indica  2759 51.20% 2.40% 1.30% 45.13% NA
All Japonica  1512 97.80% 0.10% 0.07% 2.05% NA
Aus  269 13.80% 50.20% 15.61% 20.45% NA
Indica I  595 20.80% 1.70% 2.18% 75.29% NA
Indica II  465 51.00% 0.20% 0.43% 48.39% NA
Indica III  913 69.20% 3.10% 0.88% 26.83% NA
Indica Intermediate  786 53.40% 3.30% 1.65% 41.60% NA
Temperate Japonica  767 98.60% 0.00% 0.00% 1.43% NA
Tropical Japonica  504 97.80% 0.00% 0.00% 2.18% NA
Japonica Intermediate  241 95.00% 0.80% 0.41% 3.73% NA
VI/Aromatic  96 57.30% 1.00% 4.17% 37.50% NA
Intermediate  90 70.00% 1.10% 1.11% 27.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1101255723 G -> A LOC_Os11g03340.1 synonymous_variant ; p.Lys188Lys; LOW synonymous_codon Average:6.762; most accessible tissue: Callus, score: 12.962 N N N N
vg1101255723 G -> DEL LOC_Os11g03340.1 N frameshift_variant Average:6.762; most accessible tissue: Callus, score: 12.962 N N N N