Search for Variation information by Variation ID:

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

Detailed information for vg1212666270:

Variant ID: vg1212666270 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 12666270
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


AGCTGGTTGACAAAGCAATTCGCCTTGAAGACAAGAAGAACAGGATGGATAACCGTAAAAGGAAAATGACTGTTTTCCAGGAGGCACAAGGTAGTAGCCA[G/A]
AGGCAGCGTATCAAGCCACTCCAAATTGGTGAATCTTCTTCCGCTGGTCAAGGACAGTCGCAACTGTTGAACATCGGTGGTGAGATCAAATTAGAGACTA

Reverse complement sequence

TAGTCTCTAATTTGATCTCACCACCGATGTTCAACAGTTGCGACTGTCCTTGACCAGCGGAAGAAGATTCACCAATTTGGAGTGGCTTGATACGCTGCCT[C/T]
TGGCTACTACCTTGTGCCTCCTGGAAAACAGTCATTTTCCTTTTACGGTTATCCATCCTGTTCTTCTTGTCTTCAAGGCGAATTGCTTTGTCAACCAGCT

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 79.50% 0.10% 1.52% 18.90% NA
All Indica  2759 83.30% 0.00% 1.27% 15.40% NA
All Japonica  1512 69.80% 0.10% 1.85% 28.31% NA
Aus  269 94.10% 0.40% 0.37% 5.20% NA
Indica I  595 70.60% 0.00% 2.02% 27.39% NA
Indica II  465 83.40% 0.00% 1.29% 15.27% NA
Indica III  913 91.50% 0.00% 0.55% 8.00% NA
Indica Intermediate  786 83.50% 0.00% 1.53% 15.01% NA
Temperate Japonica  767 83.60% 0.00% 0.13% 16.30% NA
Tropical Japonica  504 57.70% 0.00% 3.57% 38.69% NA
Japonica Intermediate  241 51.00% 0.40% 3.73% 44.81% NA
VI/Aromatic  96 82.30% 4.20% 3.12% 10.42% NA
Intermediate  90 76.70% 0.00% 5.56% 17.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1212666270 G -> DEL LOC_Os12g22430.1 N frameshift_variant Average:4.447; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg1212666270 G -> A LOC_Os12g22430.1 synonymous_variant ; p.Gln245Gln; LOW synonymous_codon Average:4.447; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N