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Detailed information for vg0611474656:

Variant ID: vg0611474656 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 11474656
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGAGGACGAAGCCATAGCCCTTAGATCTACCAGATTGCTTGTTGGAGATGACACAGCAGTCCTCGAGCTCACCGAAGAGGGAGAACGCAAAGTGGAGGTC[G/A]
TCGGCTTCGGCGCCCCAGCCGAGGCCGTGGACGAAGAGCTTCATGCTCGTGAGGTCGGCCTCCGTTGCACATAGCACAACCGCCATCGTCGCAGGGGTCG

Reverse complement sequence

CGACCCCTGCGACGATGGCGGTTGTGCTATGTGCAACGGAGGCCGACCTCACGAGCATGAAGCTCTTCGTCCACGGCCTCGGCTGGGGCGCCGAAGCCGA[C/T]
GACCTCCACTTTGCGTTCTCCCTCTTCGGTGAGCTCGAGGACTGCTGTGTCATCTCCAACAAGCAATCTGGTAGATCTAAGGGCTATGGCTTCGTCCTCT

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 95.00% 5.00% 0.00% 0.00% NA
All Indica  2759 91.70% 8.30% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 77.80% 22.20% 0.00% 0.00% NA
Indica Intermediate  786 96.90% 3.10% 0.00% 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 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg0611474656 G -> A LOC_Os06g20010.1 synonymous_variant ; p.Asp29Asp; LOW synonymous_codon Average:73.711; most accessible tissue: Zhenshan97 young leaf, score: 90.815 N N N N