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Detailed information for vg0118270542:

Variant ID: vg0118270542 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 18270542
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 300. )

Flanking Sequence (100 bp) in Reference Genome:


CACCAATGGAGGTTGCGGTACGAGAGATTGCTACGCACTGGTTCGAGGACCAGCGAGCGAGTAGAATCATCTCTCAAACACCAATGGAGGTTGCGGTGCG[G/A]
GAGATTGCTACGTACTGGTTCGAGAACCAGCGAGCAAGTAGAATCATCTCTCGAACACCAATGGAGGTTGCGGTGCGGGAGATTGCTACGTACTGGTTCA

Reverse complement sequence

TGAACCAGTACGTAGCAATCTCCCGCACCGCAACCTCCATTGGTGTTCGAGAGATGATTCTACTTGCTCGCTGGTTCTCGAACCAGTACGTAGCAATCTC[C/T]
CGCACCGCAACCTCCATTGGTGTTTGAGAGATGATTCTACTCGCTCGCTGGTCCTCGAACCAGTGCGTAGCAATCTCTCGTACCGCAACCTCCATTGGTG

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 87.70% 4.00% 8.34% 0.00% NA
All Indica  2759 80.10% 6.70% 13.16% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 91.10% 0.00% 8.92% 0.00% NA
Indica I  595 64.90% 12.40% 22.69% 0.00% NA
Indica II  465 66.20% 10.30% 23.44% 0.00% NA
Indica III  913 97.00% 1.80% 1.20% 0.00% NA
Indica Intermediate  786 80.20% 6.10% 13.74% 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  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 90.00% 2.20% 7.78% 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
vg0118270542 G -> A LOC_Os01g33180.1 synonymous_variant ; p.Arg32Arg; LOW synonymous_codon Average:55.37; most accessible tissue: Minghui63 young leaf, score: 74.514 N N N N