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Detailed information for vg1227342230:

Variant ID: vg1227342230 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 27342230
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, T: 0.04, others allele: 0.00, population size: 336. )

Flanking Sequence (100 bp) in Reference Genome:


TTCCACCAATGCTCTTCTTCCTGGACAGAAGACATATCCAGAGGAAGCCTAGTACCGCGATCAATGCAAGAGCCATGGTTGACATTGAGCCAATCACAAT[G/T]
CCATTCAGGAAGTGCGATGTTTTGTTGTTGTTGATTGGTGAAACGCCTGTTTGCGACAGAGAGATGAAACCATCAGTTAGTCACACACACATTGCACCAA

Reverse complement sequence

TTGGTGCAATGTGTGTGTGACTAACTGATGGTTTCATCTCTCTGTCGCAAACAGGCGTTTCACCAATCAACAACAACAAAACATCGCACTTCCTGAATGG[C/A]
ATTGTGATTGGCTCAATGTCAACCATGGCTCTTGCATTGATCGCGGTACTAGGCTTCCTCTGGATATGTCTTCTGTCCAGGAAGAAGAGCATTGGTGGAA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 75.30% 24.50% 0.13% 0.00% NA
All Indica  2759 59.00% 40.80% 0.22% 0.00% NA
All Japonica  1512 99.60% 0.40% 0.00% 0.00% NA
Aus  269 94.40% 5.60% 0.00% 0.00% NA
Indica I  595 82.00% 17.60% 0.34% 0.00% NA
Indica II  465 77.20% 22.80% 0.00% 0.00% NA
Indica III  913 38.70% 61.10% 0.22% 0.00% NA
Indica Intermediate  786 54.50% 45.30% 0.25% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 85.60% 14.40% 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
vg1227342230 G -> T LOC_Os12g44090.1 synonymous_variant ; p.Gly268Gly; LOW synonymous_codon Average:61.897; most accessible tissue: Zhenshan97 panicle, score: 84.374 N N N N