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Detailed information for vg0303700315:

Variant ID: vg0303700315 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 3700315
Reference Allele: CAlternative Allele: A
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, C: 0.02, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:


TTGAGAGGAGAACATAATCACCGCTTTCATCATTCCTTGCCTTTAGCAGTTGCCTATTTGCATGTTTAGCCAGTTCGATCTCACCATGAACCCTACAAGC[C/A]
GAAAGTAGTGTTCTCCAAATGACAGAATTAGGCTCACATTTCATCGTATCAATGAACTCAAATGCTTCTTTTAGTAGCCCAGCACGACCCAGCATGTCCA

Reverse complement sequence

TGGACATGCTGGGTCGTGCTGGGCTACTAAAAGAAGCATTTGAGTTCATTGATACGATGAAATGTGAGCCTAATTCTGTCATTTGGAGAACACTACTTTC[G/T]
GCTTGTAGGGTTCATGGTGAGATCGAACTGGCTAAACATGCAAATAGGCAACTGCTAAAGGCAAGGAATGATGAAAGCGGTGATTATGTTCTCCTCTCAA

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 65.00% 34.90% 0.02% 0.00% NA
All Indica  2759 98.20% 1.80% 0.00% 0.00% NA
All Japonica  1512 0.50% 99.50% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 98.80% 1.20% 0.00% 0.00% NA
Indica II  465 95.10% 4.90% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 97.70% 2.30% 0.00% 0.00% NA
Temperate Japonica  767 0.40% 99.60% 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 45.80% 54.20% 0.00% 0.00% NA
Intermediate  90 50.00% 48.90% 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
vg0303700315 C -> A LOC_Os03g07234.1 synonymous_variant ; p.Ser424Ser; LOW synonymous_codon Average:53.505; most accessible tissue: Zhenshan97 young leaf, score: 79.507 N N N N