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Detailed information for vg0303700300:

Variant ID: vg0303700300 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 3700300
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.95, G: 0.05, others allele: 0.00, population size: 331. )

Flanking Sequence (100 bp) in Reference Genome:


CAGATGCATAGATGTTTGAGAGGAGAACATAATCACCGCTTTCATCATTCCTTGCCTTTAGCAGTTGCCTATTTGCATGTTTAGCCAGTTCGATCTCACC[A/G]
TGAACCCTACAAGCCGAAAGTAGTGTTCTCCAAATGACAGAATTAGGCTCACATTTCATCGTATCAATGAACTCAAATGCTTCTTTTAGTAGCCCAGCAC

Reverse complement sequence

GTGCTGGGCTACTAAAAGAAGCATTTGAGTTCATTGATACGATGAAATGTGAGCCTAATTCTGTCATTTGGAGAACACTACTTTCGGCTTGTAGGGTTCA[T/C]
GGTGAGATCGAACTGGCTAAACATGCAAATAGGCAACTGCTAAAGGCAAGGAATGATGAAAGCGGTGATTATGTTCTCCTCTCAAACATCTATGCATCTG

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 98.60% 1.40% 0.02% 0.00% NA
All Indica  2759 99.60% 0.40% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 85.10% 14.90% 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 99.30% 0.70% 0.00% 0.00% NA
Indica Intermediate  786 99.40% 0.60% 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 92.70% 7.30% 0.00% 0.00% NA
Intermediate  90 91.10% 7.80% 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
vg0303700300 A -> G LOC_Os03g07234.1 synonymous_variant ; p.His429His; LOW synonymous_codon Average:53.02; most accessible tissue: Zhenshan97 young leaf, score: 79.783 N N N N