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Detailed information for vg0302708845:

Variant ID: vg0302708845 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 2708845
Reference Allele: CAlternative Allele: A
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.73, A: 0.28, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:


TAAGCTCACAAGGTTCTAGCAGTGGAAGCAATTTTGAGATGCGGAGATCAATGAAAGGACTGTATAATCCAATGCATAGAAATTCTTCAGGAAAGGAGAT[C/A]
CCTGGAAGCACACAGTTCTCCTTACCACAGATCCAGAAAGCAACCAAAAATTTCTCGCCAAACCTGAAGATTGGGCAGGGCGGTTCCGGGACAGTATACA

Reverse complement sequence

TGTATACTGTCCCGGAACCGCCCTGCCCAATCTTCAGGTTTGGCGAGAAATTTTTGGTTGCTTTCTGGATCTGTGGTAAGGAGAACTGTGTGCTTCCAGG[G/T]
ATCTCCTTTCCTGAAGAATTTCTATGCATTGGATTATACAGTCCTTTCATTGATCTCCGCATCTCAAAATTGCTTCCACTGCTAGAACCTTGTGAGCTTA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 64.70% 35.30% 0.02% 0.00% NA
All Indica  2759 97.40% 2.50% 0.04% 0.00% NA
All Japonica  1512 0.50% 99.50% 0.00% 0.00% NA
Aus  269 97.80% 2.20% 0.00% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 94.60% 5.40% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 94.50% 5.30% 0.13% 0.00% NA
Temperate Japonica  767 0.50% 99.50% 0.00% 0.00% NA
Tropical Japonica  504 0.40% 99.60% 0.00% 0.00% NA
Japonica Intermediate  241 0.80% 99.20% 0.00% 0.00% NA
VI/Aromatic  96 54.20% 45.80% 0.00% 0.00% NA
Intermediate  90 52.20% 47.80% 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
vg0302708845 C -> A LOC_Os03g05470.1 synonymous_variant ; p.Ile122Ile; LOW synonymous_codon Average:65.451; most accessible tissue: Minghui63 young leaf, score: 81.5 N N N N