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Detailed information for vg0611474584:

Variant ID: vg0611474584 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 11474584
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGAGACGGTGGAAGAGAGGGTTGACAACGCTCCCTACGCCTCTCTCCTTCCCCTTTTCGGCATATGGGTAGAAGAGGACGAAGCCATAGCCCTTAGATCT[A/G]
CCAGATTGCTTGTTGGAGATGACACAGCAGTCCTCGAGCTCACCGAAGAGGGAGAACGCAAAGTGGAGGTCGTCGGCTTCGGCGCCCCAGCCGAGGCCGT

Reverse complement sequence

ACGGCCTCGGCTGGGGCGCCGAAGCCGACGACCTCCACTTTGCGTTCTCCCTCTTCGGTGAGCTCGAGGACTGCTGTGTCATCTCCAACAAGCAATCTGG[T/C]
AGATCTAAGGGCTATGGCTTCGTCCTCTTCTACCCATATGCCGAAAAGGGGAAGGAGAGAGGCGTAGGGAGCGTTGTCAACCCTCTCTTCCACCGTCTCA

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 99.60% 0.40% 0.00% 0.00% NA
All Indica  2759 99.30% 0.70% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 97.90% 2.10% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 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  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0611474584 A -> G LOC_Os06g20010.1 synonymous_variant ; p.Gly53Gly; LOW N Average:73.163; most accessible tissue: Zhenshan97 young leaf, score: 90.175 N N N N
vg0611474584 A -> G LOC_Os06g20000.1 upstream_gene_variant ; 4855.0bp to feature; MODIFIER N Average:73.163; most accessible tissue: Zhenshan97 young leaf, score: 90.175 N N N N
vg0611474584 A -> G LOC_Os06g20020.1 upstream_gene_variant ; 1920.0bp to feature; MODIFIER N Average:73.163; most accessible tissue: Zhenshan97 young leaf, score: 90.175 N N N N