Search for Variation information by Variation ID:

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

Detailed information for vg1216386902:

Variant ID: vg1216386902 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 16386902
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTACATTGATCCAGAAAACTTCTCATTAATGAACAAGTGGACCCAATGTATCTTGTTTTCGAAAGGAAGTCCATCAAAAGCTCTAGCAATGTGAGGGTTG[G/A]
CAACCAAATGAGCATAGTAAACAGATACATGGATCTCCTCAAACCCAGGAAGGCTTTTCAAGGTTTGAAATAAACCATCTGGCAGTTTATTGTCTGGCTC

Reverse complement sequence

GAGCCAGACAATAAACTGCCAGATGGTTTATTTCAAACCTTGAAAAGCCTTCCTGGGTTTGAGGAGATCCATGTATCTGTTTACTATGCTCATTTGGTTG[C/T]
CAACCCTCACATTGCTAGAGCTTTTGATGGACTTCCTTTCGAAAACAAGATACATTGGGTCCACTTGTTCATTAATGAGAAGTTTTCTGGATCAATGTAG

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 98.70% 0.00% 0.68% 0.55% NA
All Indica  2759 98.00% 0.10% 1.16% 0.72% NA
All Japonica  1512 99.60% 0.00% 0.00% 0.40% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 96.10% 0.00% 3.53% 0.34% NA
Indica II  465 99.60% 0.00% 0.22% 0.22% NA
Indica III  913 98.50% 0.10% 0.44% 0.99% NA
Indica Intermediate  786 98.10% 0.10% 0.76% 1.02% NA
Temperate Japonica  767 99.60% 0.00% 0.00% 0.39% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 0.00% 0.00% 1.24% 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
vg1216386902 G -> A LOC_Os12g27800.1 missense_variant ; p.Ala549Val; MODERATE N Average:11.011; most accessible tissue: Minghui63 panicle, score: 20.733 N N N N
vg1216386902 G -> A LOC_Os12g27810.1 upstream_gene_variant ; 4523.0bp to feature; MODIFIER N Average:11.011; most accessible tissue: Minghui63 panicle, score: 20.733 N N N N
vg1216386902 G -> A LOC_Os12g27790.1 downstream_gene_variant ; 2880.0bp to feature; MODIFIER N Average:11.011; most accessible tissue: Minghui63 panicle, score: 20.733 N N N N