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Detailed information for vg0703429870:

Variant ID: vg0703429870 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 3429870
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.96, C: 0.03, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:


CCATTCTTCTGAAGACAGCGATCTGGGAAGCGAAGCCTGGTTCATCGCCTGATCCGCCAACGCCACTGAACTCGACGCTGTAGTTGTGCTTTTCTGCGAG[T/C]
CCGGTAGCCCAGTGCTGGAACTGGGATCTTGTCCACTCGAACTTGTGGTCATGGTTTCGGAACTTGCAAGGACCAGCGTTTTCTTCTGGTTCTTCTTCCT

Reverse complement sequence

AGGAAGAAGAACCAGAAGAAAACGCTGGTCCTTGCAAGTTCCGAAACCATGACCACAAGTTCGAGTGGACAAGATCCCAGTTCCAGCACTGGGCTACCGG[A/G]
CTCGCAGAAAAGCACAACTACAGCGTCGAGTTCAGTGGCGTTGGCGGATCAGGCGATGAACCAGGCTTCGCTTCCCAGATCGCTGTCTTCAGAAGAATGG

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 99.60% 0.40% 0.00% 0.00% NA
All Indica  2759 99.50% 0.50% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 97.00% 3.00% 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 99.60% 0.40% 0.00% 0.00% NA
Indica Intermediate  786 98.90% 1.10% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0703429870 T -> C LOC_Os07g06970.1 synonymous_variant ; p.Gly862Gly; LOW synonymous_codon Average:79.921; most accessible tissue: Zhenshan97 young leaf, score: 87.299 N N N N