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Detailed information for vg0327370221:

Variant ID: vg0327370221 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 27370221
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.72, T: 0.28, others allele: 0.00, population size: 191. )

Flanking Sequence (100 bp) in Reference Genome:


AACTCTCAATCCGCTTTTTTATCTCTTCGATAATTAACGGGAAATCCCGCCTAAGATGAAAGTAGCCATCAGTGACGGCCACCTTCTTGAAGTTGATCTC[C/T]
GCCATCAAGAAGCTGAGCCACTTGCTCTTTAGCTCCGGGCAATGGTACCTCTCGGCGTAGGCGCGTAGCCTAGAGTCATCGCCACCGTCTCCACCGACAC

Reverse complement sequence

GTGTCGGTGGAGACGGTGGCGATGACTCTAGGCTACGCGCCTACGCCGAGAGGTACCATTGCCCGGAGCTAAAGAGCAAGTGGCTCAGCTTCTTGATGGC[G/A]
GAGATCAACTTCAAGAAGGTGGCCGTCACTGATGGCTACTTTCATCTTAGGCGGGATTTCCCGTTAATTATCGAAGAGATAAAAAAGCGGATTGAGAGTT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 64.40% 35.30% 0.02% 0.23% NA
All Indica  2759 97.80% 1.90% 0.04% 0.25% NA
All Japonica  1512 1.20% 98.60% 0.00% 0.20% NA
Aus  269 96.70% 3.30% 0.00% 0.00% NA
Indica I  595 99.00% 0.80% 0.00% 0.17% NA
Indica II  465 98.30% 1.10% 0.00% 0.65% NA
Indica III  913 97.20% 2.60% 0.11% 0.11% NA
Indica Intermediate  786 97.30% 2.40% 0.00% 0.25% NA
Temperate Japonica  767 0.50% 99.20% 0.00% 0.26% NA
Tropical Japonica  504 1.80% 98.00% 0.00% 0.20% NA
Japonica Intermediate  241 2.10% 97.90% 0.00% 0.00% NA
VI/Aromatic  96 16.70% 83.30% 0.00% 0.00% NA
Intermediate  90 57.80% 41.10% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0327370221 C -> T LOC_Os03g48120.1 synonymous_variant ; p.Ala170Ala; LOW synonymous_codon Average:77.274; most accessible tissue: Zhenshan97 panicle, score: 86.788 N N N N
vg0327370221 C -> DEL LOC_Os03g48120.1 N frameshift_variant Average:77.274; most accessible tissue: Zhenshan97 panicle, score: 86.788 N N N N