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Detailed information for vg0627801785:

Variant ID: vg0627801785 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 27801785
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:


TATAGTAGGAAAATATCTAAGTGTACAGCCTTTACTTTCTCGAATAGTAACTCTTCCGAATATTCTTGCGCGATGATATTTTTCCATATATGTACACAGG[A/G]
CAAAAATGATGGAGATTGGTGGCTTTACTTTGGATATGACATCAACAATCTCAATCGAGTTGGATTTTGGCCAAAGAATATTTTTAATCGTATGGTAGAT

Reverse complement sequence

ATCTACCATACGATTAAAAATATTCTTTGGCCAAAATCCAACTCGATTGAGATTGTTGATGTCATATCCAAAGTAAAGCCACCAATCTCCATCATTTTTG[T/C]
CCTGTGTACATATATGGAAAAATATCATCGCGCAAGAATATTCGGAAGAGTTACTATTCGAGAAAGTAAAGGCTGTACACTTAGATATTTTCCTACTATA

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 98.90% 1.10% 0.02% 0.00% NA
All Indica  2759 98.30% 1.70% 0.04% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 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 95.20% 4.70% 0.11% 0.00% NA
Indica Intermediate  786 99.60% 0.40% 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 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0627801785 A -> G LOC_Os06g45920.1 missense_variant&splice_region_variant ; p.Asp118Gly; MODERATE nonsynonymous_codon ; D118G Average:57.078; most accessible tissue: Callus, score: 80.193 unknown unknown TOLERATED 0.16