Search for Variation information by Variation ID:

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

Detailed information for vg0135984016:

Variant ID: vg0135984016 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 35984016
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 327. )

Flanking Sequence (100 bp) in Reference Genome:


GTTAGCAGATCAGTACTCCCAGTTTGCAATGTCCTTTGAACATTTGCCACGGGTTAGTGGTAGGTGCAGCTTAACTGGCGATCATTGTCATCCTAAGAAG[G/T]
TTGTGGTCGGCACACTTGTTACTCTTGTGGTTTCATGTCGATCTTGGCTGTAATCGAGCACAGTAACCATGTAGCAACATGTTTCTGCTCAAAGACGAGC

Reverse complement sequence

GCTCGTCTTTGAGCAGAAACATGTTGCTACATGGTTACTGTGCTCGATTACAGCCAAGATCGACATGAAACCACAAGAGTAACAAGTGTGCCGACCACAA[C/A]
CTTCTTAGGATGACAATGATCGCCAGTTAAGCTGCACCTACCACTAACCCGTGGCAAATGTTCAAAGGACATTGCAAACTGGGAGTACTGATCTGCTAAC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.20% 1.80% 0.00% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 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  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 26.00% 74.00% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 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
vg0135984016 G -> T LOC_Os01g62160.1 3_prime_UTR_variant ; 371.0bp to feature; MODIFIER silent_mutation Average:74.332; most accessible tissue: Zhenshan97 flower, score: 85.482 N N N N