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Detailed information for vg0106164859:

Variant ID: vg0106164859 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 6164859
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTCTTTCTGAGTATAGCCCTTAGCAACAAGCCGAGCCTTGTACTTTTCAATAGTACCGTCAGGCCTAAGCTTCTTCTTGAACACCCACTTGCACCCCACA[G/A]
GTTTACACCCACCATGCCTTAGGCAGTCCCGCGGTGTCCAACATGGCATTCACCAAGTCAGTCAGTGTGCGGTTCTTCCTTTCAGCAATCCCATTAGACT

Reverse complement sequence

AGTCTAATGGGATTGCTGAAAGGAAGAACCGCACACTGACTGACTTGGTGAATGCCATGTTGGACACCGCGGGACTGCCTAAGGCATGGTGGGTGTAAAC[C/T]
TGTGGGGTGCAAGTGGGTGTTCAAGAAGAAGCTTAGGCCTGACGGTACTATTGAAAAGTACAAGGCTCGGCTTGTTGCTAAGGGCTATACTCAGAAAGAA

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 22.40% 0.30% 14.73% 62.53% NA
All Indica  2759 1.20% 0.00% 18.41% 80.36% NA
All Japonica  1512 63.60% 1.10% 7.01% 28.31% NA
Aus  269 1.10% 0.00% 20.45% 78.44% NA
Indica I  595 0.20% 0.00% 6.55% 93.28% NA
Indica II  465 1.30% 0.00% 9.89% 88.82% NA
Indica III  913 0.90% 0.00% 30.01% 69.11% NA
Indica Intermediate  786 2.40% 0.00% 18.96% 78.63% NA
Temperate Japonica  767 92.40% 2.10% 1.30% 4.17% NA
Tropical Japonica  504 30.40% 0.00% 11.11% 58.53% NA
Japonica Intermediate  241 41.50% 0.00% 16.60% 41.91% NA
VI/Aromatic  96 40.60% 0.00% 11.46% 47.92% NA
Intermediate  90 23.30% 0.00% 17.78% 58.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0106164859 G -> A LOC_Os01g11450.1 intron_variant ; MODIFIER silent_mutation Average:4.816; most accessible tissue: Zhenshan97 young leaf, score: 8.295 N N N N
vg0106164859 G -> DEL N N silent_mutation Average:4.816; most accessible tissue: Zhenshan97 young leaf, score: 8.295 N N N N