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Detailed information for vg0703430671:

Variant ID: vg0703430671 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 3430671
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.01, others allele: 0.00, population size: 336. )

Flanking Sequence (100 bp) in Reference Genome:


AAGGGATGGTTTAAAGGGTGAACTAACTATCAACAGTCATCAAGGCTCTGTTACGTGCCTTTGCTGCTCGTGTGAGACCCTTCCGAGAAATGTCAACACC[G/A]
ACAACTTTTTCAAGGGTTGTTGGATGCTCAAGCAATGAATCAAGAAGGCTACCAGATCCACAGCCAAAATCAACCTGAACAAATTTACTTCAATAGTGAT

Reverse complement sequence

ATCACTATTGAAGTAAATTTGTTCAGGTTGATTTTGGCTGTGGATCTGGTAGCCTTCTTGATTCATTGCTTGAGCATCCAACAACCCTTGAAAAAGTTGT[C/T]
GGTGTTGACATTTCTCGGAAGGGTCTCACACGAGCAGCAAAGGCACGTAACAGAGCCTTGATGACTGTTGATAGTTAGTTCACCCTTTAAACCATCCCTT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.50% 0.50% 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 97.80% 2.20% 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
vg0703430671 G -> A LOC_Os07g06970.1 synonymous_variant ; p.Val725Val; LOW synonymous_codon Average:56.721; most accessible tissue: Minghui63 flower, score: 71.461 N N N N