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Detailed information for vg0919120357:

Variant ID: vg0919120357 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 19120357
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:


CAGTGAGGATGATGAAGAACCTCGTCCAGTAAACGAGCGGCTTCACAAATAGTACACGAATATCCGCAGCCTTCACCTCGCTTGCAACTTTAGCTAGGGA[G/A]
ACAGCAACTGAAGAGAACACAAAGATATGTTCAAGCTTCAGGGATTTTGTATTTTGGACCGTTAAAGAAAAAAATATTATAAAGCAAGTGAGTACGAATC

Reverse complement sequence

GATTCGTACTCACTTGCTTTATAATATTTTTTTCTTTAACGGTCCAAAATACAAAATCCCTGAAGCTTGAACATATCTTTGTGTTCTCTTCAGTTGCTGT[C/T]
TCCCTAGCTAAAGTTGCAAGCGAGGTGAAGGCTGCGGATATTCGTGTACTATTTGTGAAGCCGCTCGTTTACTGGACGAGGTTCTTCATCATCCTCACTG

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 99.80% 0.10% 0.04% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 99.30% 0.70% 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  913 100.00% 0.00% 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 97.90% 1.00% 1.04% 0.00% NA
Intermediate  90 95.60% 3.30% 1.11% 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
vg0919120357 G -> A LOC_Os09g32030.1 synonymous_variant ; p.Val115Val; LOW synonymous_codon Average:62.02; most accessible tissue: Minghui63 flower, score: 73.172 N N N N