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Detailed information for vg0704594140:

Variant ID: vg0704594140 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 4594140
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, A: 0.03, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:


TCATTACCTTGACTGCCATATAATGGCACACCACACCACTTGGATTTGTTAATCCAAATCGTTAACAAAAGCATGAGCATTAGTAATCCAAAACTAACGA[C/A]
AATGCTTACAATGGCAACAACTCTTGGTCTCCGTTTGTTGTTCTTCCTTAAACTTTGTGAATCTCTGGCGGCGAGGCGAAGGTAAAGAACATTTTCAGAA

Reverse complement sequence

TTCTGAAAATGTTCTTTACCTTCGCCTCGCCGCCAGAGATTCACAAAGTTTAAGGAAGAACAACAAACGGAGACCAAGAGTTGTTGCCATTGTAAGCATT[G/T]
TCGTTAGTTTTGGATTACTAATGCTCATGCTTTTGTTAACGATTTGGATTAACAAATCCAAGTGGTGTGGTGTGCCATTATATGGCAGTCAAGGTAATGA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.90% 0.10% 0.00% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 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 99.70% 0.30% 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
vg0704594140 C -> A LOC_Os07g08860.1 missense_variant ; p.Val490Phe; MODERATE N Average:47.903; most accessible tissue: Zhenshan97 panicle, score: 59.59 N N N N
vg0704594140 C -> A LOC_Os07g08850.1 downstream_gene_variant ; 3474.0bp to feature; MODIFIER N Average:47.903; most accessible tissue: Zhenshan97 panicle, score: 59.59 N N N N
vg0704594140 C -> A LOC_Os07g08870.1 downstream_gene_variant ; 2266.0bp to feature; MODIFIER N Average:47.903; most accessible tissue: Zhenshan97 panicle, score: 59.59 N N N N