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Detailed information for vg1105160867:

Variant ID: vg1105160867 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 5160867
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTGCCGTGCCGTCATGACCAAGTTGGCCACGTCGTCCAGCCAACGTTGGGCTGGAGACTCCGGGTCAGGGACAATGGGCGGGTGACGTAGGAGCGCGCCC[G/A]
CAGCTTGGAGCGCGCCCTGGGGCGTGCTGCCGTCGCCGTAGACGAGGAGGCGACGCTCCCCACCTCGCCGCCCTTCCCCATCACCCGTGGATGTCGAAGT

Reverse complement sequence

ACTTCGACATCCACGGGTGATGGGGAAGGGCGGCGAGGTGGGGAGCGTCGCCTCCTCGTCTACGGCGACGGCAGCACGCCCCAGGGCGCGCTCCAAGCTG[C/T]
GGGCGCGCTCCTACGTCACCCGCCCATTGTCCCTGACCCGGAGTCTCCAGCCCAACGTTGGCTGGACGACGTGGCCAACTTGGTCATGACGGCACGGCAG

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 33.50% 0.20% 14.56% 51.78% NA
All Indica  2759 9.90% 0.30% 19.06% 70.71% NA
All Japonica  1512 83.80% 0.00% 2.65% 13.56% NA
Aus  269 0.70% 0.00% 28.25% 71.00% NA
Indica I  595 6.10% 0.00% 6.39% 87.56% NA
Indica II  465 5.20% 1.50% 14.19% 79.14% NA
Indica III  913 8.20% 0.00% 34.06% 57.72% NA
Indica Intermediate  786 17.60% 0.30% 14.12% 68.07% NA
Temperate Japonica  767 88.70% 0.00% 0.65% 10.69% NA
Tropical Japonica  504 79.00% 0.00% 3.57% 17.46% NA
Japonica Intermediate  241 78.40% 0.00% 7.05% 14.52% NA
VI/Aromatic  96 9.40% 0.00% 36.46% 54.17% NA
Intermediate  90 34.40% 0.00% 12.22% 53.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1105160867 G -> A LOC_Os11g09660.1 missense_variant ; p.Ala85Val; MODERATE nonsynonymous_codon ; A85V Average:6.486; most accessible tissue: Zhenshan97 panicle, score: 16.188 benign 0.382 TOLERATED 0.07
vg1105160867 G -> DEL LOC_Os11g09660.1 N frameshift_variant Average:6.486; most accessible tissue: Zhenshan97 panicle, score: 16.188 N N N N