Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1007739818:

Variant ID: vg1007739818 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 7739818
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


ACATCTTGTGTATTAGGTTCTGCCATGCCTGCGGCTTGGGGGAGTTGGAGGTGATGGTGAACGCTGCCATCTCCTCCAAGCAGCTCTCAAGAAACACACG[A/C]
ACCTCCATATCGGTCCACCGGCTACGGCCATCGCCCATCTACTCCGTGCAAGTCAAATAAAATTGAATCGGAAATGAACAAATTAATACAAACAAATACC

Reverse complement sequence

GGTATTTGTTTGTATTAATTTGTTCATTTCCGATTCAATTTTATTTGACTTGCACGGAGTAGATGGGCGATGGCCGTAGCCGGTGGACCGATATGGAGGT[T/G]
CGTGTGTTTCTTGAGAGCTGCTTGGAGGAGATGGCAGCGTTCACCATCACCTCCAACTCCCCCAAGCCGCAGGCATGGCAGAACCTAATACACAAGATGT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.70% 0.60% 0.61% 6.09% NA
All Indica  2759 98.60% 0.50% 0.33% 0.58% NA
All Japonica  1512 80.70% 0.50% 1.06% 17.72% NA
Aus  269 95.90% 2.60% 1.49% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.30% 0.00% 0.43% 1.29% NA
Indica III  913 97.90% 1.30% 0.22% 0.55% NA
Indica Intermediate  786 98.60% 0.10% 0.64% 0.64% NA
Temperate Japonica  767 82.00% 0.00% 0.78% 17.21% NA
Tropical Japonica  504 81.50% 1.40% 1.79% 15.28% NA
Japonica Intermediate  241 74.70% 0.40% 0.41% 24.48% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 0.00% 0.00% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1007739818 A -> C LOC_Os10g14290.1 synonymous_variant ; p.Val122Val; LOW synonymous_codon Average:5.203; most accessible tissue: Callus, score: 12.568 N N N N
vg1007739818 A -> DEL LOC_Os10g14290.1 N frameshift_variant Average:5.203; most accessible tissue: Callus, score: 12.568 N N N N