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Detailed information for vg0611474533:

Variant ID: vg0611474533 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 11474533
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 322. )

Flanking Sequence (100 bp) in Reference Genome:


TCTCCCCTCTACCCCGGGCAGTCTTCTTCCTCCTCTCTCCCTACTCCTCTCTGAGACGGTGGAAGAGAGGGTTGACAACGCTCCCTACGCCTCTCTCCTT[C/A]
CCCTTTTCGGCATATGGGTAGAAGAGGACGAAGCCATAGCCCTTAGATCTACCAGATTGCTTGTTGGAGATGACACAGCAGTCCTCGAGCTCACCGAAGA

Reverse complement sequence

TCTTCGGTGAGCTCGAGGACTGCTGTGTCATCTCCAACAAGCAATCTGGTAGATCTAAGGGCTATGGCTTCGTCCTCTTCTACCCATATGCCGAAAAGGG[G/T]
AAGGAGAGAGGCGTAGGGAGCGTTGTCAACCCTCTCTTCCACCGTCTCAGAGAGGAGTAGGGAGAGAGGAGGAAGAAGACTGCCCGGGGTAGAGGGGAGA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.50% 4.50% 0.00% 0.00% NA
All Indica  2759 92.40% 7.60% 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 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 79.80% 20.20% 0.00% 0.00% NA
Indica Intermediate  786 97.10% 2.90% 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 98.90% 1.10% 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
vg0611474533 C -> A LOC_Os06g20010.1 synonymous_variant ; p.Gly70Gly; LOW synonymous_codon Average:72.551; most accessible tissue: Zhenshan97 young leaf, score: 87.859 N N N N