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Detailed information for vg0200563021:

Variant ID: vg0200563021 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 563021
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:


TGTCATCAACGCCTTTCTTCATCAGCTGCCTGAAGAAAGTCTCAGCCTTGCTGGTGTTCCCATTGCTGCACAAATACTCAATCACTGGATTATAAGCTGG[C/T]
CCTTCAAGCACAGGGCTCTTTGGGCTCAACAGTGTCCCCTTCTCAAGAAGCTCATCCATCACCTCAACAGCACCATCACACTTTCCACCCGCGCACAAGC

Reverse complement sequence

GCTTGTGCGCGGGTGGAAAGTGTGATGGTGCTGTTGAGGTGATGGATGAGCTTCTTGAGAAGGGGACACTGTTGAGCCCAAAGAGCCCTGTGCTTGAAGG[G/A]
CCAGCTTATAATCCAGTGATTGAGTATTTGTGCAGCAATGGGAACACCAGCAAGGCTGAGACTTTCTTCAGGCAGCTGATGAAGAAAGGCGTTGATGACA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.30% 1.70% 0.02% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 99.50% 0.50% 0.00% 0.00% NA
Aus  269 85.90% 14.10% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.30% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 97.90% 2.10% 0.00% 0.00% NA
VI/Aromatic  96 69.80% 30.20% 0.00% 0.00% NA
Intermediate  90 94.40% 4.40% 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
vg0200563021 C -> T LOC_Os02g02020.1 synonymous_variant ; p.Gly462Gly; LOW synonymous_codon Average:76.226; most accessible tissue: Minghui63 flag leaf, score: 83.826 N N N N